Title: Package for Sequence Analysis by Local Score
Description: Functionalities for calculating the local score and calculating statistical relevance (p-value) to find a local Score in a sequence of given distribution (S. Mercier and J.-J. Daudin (2001) <https://hal.archives-ouvertes.fr/hal-00714174> ; S. Karlin and S. Altschul (1990) <https://www.pnas.org/content/87/6/2264> ; S. Mercier, D. Cellier and F. Charlot (2003) <https://hal.archives-ouvertes.fr/hal-00937529v1> ; A. Lagnoux, S. Mercier and P. Valois (2017) <doi:10.1093/bioinformatics/btw699> ).
Author: Sebastian Simon [aut],
David Robelin [aut, cre],
Sabine Mercier [aut],
Sebastien Dejean [aut],
The authors of Eigen the library for the included version of Eigen
[cph]
Maintainer: David Robelin <david.robelin@inrae.fr>
Diff between localScore versions 1.0.4 dated 2021-02-23 and 1.0.5 dated 2021-02-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- inst/doc/localScorePackageDocumentation.pdf |binary src/pValueMethods.cpp | 12 ++++++------ 4 files changed, 12 insertions(+), 12 deletions(-)
Title: A Tool for Sensitivity Analysis in Structural Equation Modeling
Description: Perform sensitivity analysis in structural equation modeling using
meta-heuristic optimization methods (e.g., ant colony optimization and others).
The references for the proposed methods are:
(1) Leite, W., & Shen, Z., Marcoulides, K., Fish, C., & Harring, J. (in press).
Using ant colony optimization for sensitivity analysis in
structural equation modeling.
Structural Equation Modeling: A Multidisciplinary Journal.
(2) Harring, J. R., McNeish, D. M., & Hancock, G. R. (2017)
<doi:10.1080/10705511.2018.1506925>;
(3) Socha, K., & Dorigo, M. (2008) <doi:10.1016/j.ejor.2006.06.046>.
We also thank Dr. Krzysztof Socha for sharing his research on ant colony optimization
algorithm with continuous domains and associated R code,
which provided the base for the development of this package.
Author: Walter Leite [aut, cre],
Zuchao Shen [aut],
Gail Fish [ctb],
YongSeok Lee [ctb],
Sanaz Nazari [ctb],
Jia Quan [ctb],
Eric Wright [ctb],
Huibin Zhang [ctb]
Maintainer: Walter Leite <walter.leite@coe.ufl.edu>
Diff between SEMsens versions 0.2.6 dated 2020-07-18 and 1.0.1 dated 2021-02-23
SEMsens-0.2.6/SEMsens/inst/doc/SEMsens.html |only SEMsens-1.0.1/SEMsens/DESCRIPTION | 41 +- SEMsens-1.0.1/SEMsens/MD5 | 46 +- SEMsens-1.0.1/SEMsens/NEWS.md | 17 SEMsens-1.0.1/SEMsens/R/SEMsens-package.R | 10 SEMsens-1.0.1/SEMsens/R/gen.sens.pars.R | 12 SEMsens-1.0.1/SEMsens/R/sa.aco.R | 242 +++++++----- SEMsens-1.0.1/SEMsens/R/sens.tables.R | 90 +++- SEMsens-1.0.1/SEMsens/R/smith19.R |only SEMsens-1.0.1/SEMsens/build/vignette.rds |binary SEMsens-1.0.1/SEMsens/data |only SEMsens-1.0.1/SEMsens/inst/doc/Hom-vignette.R |only SEMsens-1.0.1/SEMsens/inst/doc/Hom-vignette.Rmd |only SEMsens-1.0.1/SEMsens/inst/doc/Hom-vignette.pdf |only SEMsens-1.0.1/SEMsens/inst/doc/SEMsens.R | 61 +-- SEMsens-1.0.1/SEMsens/inst/doc/SEMsens.Rmd | 88 ++-- SEMsens-1.0.1/SEMsens/inst/doc/SEMsens.pdf |only SEMsens-1.0.1/SEMsens/inst/doc/Smith12vignette.R |only SEMsens-1.0.1/SEMsens/inst/doc/Smith12vignette.Rmd |only SEMsens-1.0.1/SEMsens/inst/doc/Smith12vignette.pdf |only SEMsens-1.0.1/SEMsens/inst/doc/Smith19_6phantom3.R |only SEMsens-1.0.1/SEMsens/inst/doc/Smith19_6phantom3.Rmd |only SEMsens-1.0.1/SEMsens/inst/doc/Smith19_6phantom3.pdf |only SEMsens-1.0.1/SEMsens/man/SEMsens-package.Rd | 10 SEMsens-1.0.1/SEMsens/man/gen.sens.pars.Rd | 26 - SEMsens-1.0.1/SEMsens/man/sa.aco.Rd | 172 +++++--- SEMsens-1.0.1/SEMsens/man/sens.tables.Rd | 28 + SEMsens-1.0.1/SEMsens/man/smith19.use.Rd |only SEMsens-1.0.1/SEMsens/vignettes/Hom-vignette.Rmd |only SEMsens-1.0.1/SEMsens/vignettes/SEMsens.Rmd | 88 ++-- SEMsens-1.0.1/SEMsens/vignettes/Smith12vignette.Rmd |only SEMsens-1.0.1/SEMsens/vignettes/Smith19_6phantom3.Rmd |only SEMsens-1.0.1/SEMsens/vignettes/smith19_6_my.sa.table.rdata |only 33 files changed, 613 insertions(+), 318 deletions(-)
Title: Stochastic Approximation Expectation Maximization (SAEM)
Algorithm
Description: The SAEMIX package implements the Stochastic Approximation EM algorithm for parameter estimation in (non)linear mixed effects models. The SAEM algorithm: - computes the maximum likelihood estimator of the population parameters, without any approximation of the model (linearisation, quadrature approximation,...), using the Stochastic Approximation Expectation Maximization (SAEM) algorithm, - provides standard errors for the maximum likelihood estimator - estimates the conditional modes, the conditional means and the conditional standard deviations of the individual parameters, using the Hastings-Metropolis algorithm. Several applications of SAEM in agronomy, animal breeding and PKPD analysis have been published by members of the Monolix group. Documentation about 'saemix' is provided by a comprehensive user guide in the inst folder, and a reference concerning the methods is the paper by Comets, Lavenu and Lavielle (2017, <doi:10.18637/jss.v080.i03>). See 'citation("saemix")' for details.
Author: Emmanuelle Comets [aut, cre] (<https://orcid.org/0000-0002-9150-9886>),
Audrey Lavenu [ctb],
Marc Lavielle [ctb],
Maud Delattre [ctb]
Maintainer: Emmanuelle Comets <emmanuelle.comets@inserm.fr>
Diff between saemix versions 2.3 dated 2019-12-06 and 2.4 dated 2021-02-23
saemix-2.3/saemix/man/saemix-package.Rd |only saemix-2.3/saemix/man/z[-methods.Rd |only saemix-2.3/saemix/man/z[_--methods.Rd |only saemix-2.4/saemix/CHANGES | 16 + saemix-2.4/saemix/DESCRIPTION | 37 +- saemix-2.4/saemix/MD5 | 85 ++--- saemix-2.4/saemix/NAMESPACE | 14 saemix-2.4/saemix/R/SaemixData.R | 89 +++-- saemix-2.4/saemix/R/SaemixModel.R | 39 +- saemix-2.4/saemix/R/SaemixObject.R | 373 +++++++++++++++++++----- saemix-2.4/saemix/R/SaemixRes.R | 223 +++++++++++++- saemix-2.4/saemix/R/aaa_generics.R | 388 ++++++++++++++++++++++++- saemix-2.4/saemix/R/compute_LL.R | 22 + saemix-2.4/saemix/R/func_FIM.R | 102 +++++- saemix-2.4/saemix/R/func_aux.R | 338 +-------------------- saemix-2.4/saemix/R/func_diagnostics.R |only saemix-2.4/saemix/R/func_distcond.R | 287 +++++++++++------- saemix-2.4/saemix/R/func_estimParam.R |only saemix-2.4/saemix/R/func_plots.R | 122 +++++-- saemix-2.4/saemix/R/func_simulations.R | 3 saemix-2.4/saemix/R/main.R | 182 ++++++----- saemix-2.4/saemix/R/main_initialiseMainAlgo.R | 16 - saemix-2.4/saemix/R/main_mstep.R | 2 saemix-2.4/saemix/R/zzz.R | 2 saemix-2.4/saemix/man/PD1.saemix.Rd | 93 ++--- saemix-2.4/saemix/man/SaemixData-class.Rd | 2 saemix-2.4/saemix/man/SaemixRes-class.Rd | 18 - saemix-2.4/saemix/man/conddist.saemix.Rd | 47 +-- saemix-2.4/saemix/man/cow.saemix.Rd | 83 ++--- saemix-2.4/saemix/man/createSaemixObject.Rd |only saemix-2.4/saemix/man/initialize-methods.Rd | 2 saemix-2.4/saemix/man/kurtosis.Rd |only saemix-2.4/saemix/man/llis.saemix.Rd | 1 saemix-2.4/saemix/man/logLik.Rd | 12 saemix-2.4/saemix/man/map.saemix.Rd | 2 saemix-2.4/saemix/man/mydiag.Rd |only saemix-2.4/saemix/man/oxboys.saemix.Rd | 72 ++-- saemix-2.4/saemix/man/predict-methods.Rd | 2 saemix-2.4/saemix/man/replaceData.Rd |only saemix-2.4/saemix/man/saemix.Rd | 16 - saemix-2.4/saemix/man/saemix.internal.Rd | 24 + saemix-2.4/saemix/man/saemixControl.Rd | 2 saemix-2.4/saemix/man/saemixpredict.newdata.Rd |only saemix-2.4/saemix/man/skewness.Rd |only saemix-2.4/saemix/man/summary-methods.Rd | 5 saemix-2.4/saemix/man/testnpde.Rd | 18 - saemix-2.4/saemix/man/theo.saemix.Rd | 169 +++++----- saemix-2.4/saemix/man/vcov.Rd | 4 saemix-2.4/saemix/man/yield.saemix.Rd | 100 ++---- 49 files changed, 1913 insertions(+), 1099 deletions(-)
Title: UCA Rcmdr Plug-in
Description: Some extensions to Rcmdr (R Commander), randomness test,
variance test for one normal sample and predictions using active model,
made by R-UCA project and used in teaching statistics at University of Cadiz (UCA).
Author: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Maintainer: Manuel Munoz-Marquez <manuel.munoz@uca.es>
Diff between RcmdrPlugin.UCA versions 4.2-6 dated 2018-12-30 and 4.3-3 dated 2021-02-23
ChangeLog | 3 DESCRIPTION | 18 MD5 | 34 - NAMESPACE | 4 R/RcmdrPlugin.UCA.R | 126 +++--- build/vignette.rds |binary inst/doc/additions.R |only inst/doc/additions.html | 541 +++++++++++++++++++-------- inst/doc/adiciones.R |only inst/doc/adiciones.html | 561 ++++++++++++++++++++-------- inst/etc/menus.txt | 8 inst/po/es/LC_MESSAGES/R-RcmdrPlugin.UCA.mo |binary man/RcmdrPlugin.UCA-package.Rd | 6 man/RcmdrPlugin.UCA.es-package.Rd | 6 man/paretochartMenu.Rd |only man/paretochartMenu.es.Rd |only man/sigmaMenu.es.Rd | 6 po/R-RcmdrPlugin.UCA-es.mo |binary po/R-RcmdrPlugin.UCA-es.po | 35 + po/R-RcmdrPlugin.UCA.pot | 31 + 20 files changed, 982 insertions(+), 397 deletions(-)
More information about RcmdrPlugin.UCA at CRAN
Permanent link
Title: Assessing Skill of Climate Forecasts on Seasonal-to-Decadal
Timescales
Description: Exploits dynamical seasonal forecasts in order to provide
information relevant to stakeholders at the seasonal timescale. The package
contains process-based methods for forecast calibration, bias correction,
statistical and stochastic downscaling, optimal forecast combination and
multivariate verification, as well as basic and advanced tools to obtain
tailored products. This package was developed in the context of the
ERA4CS project MEDSCOPE and the H2020 S2S4E project.
Doblas-Reyes et al. (2005) <doi:10.1111/j.1600-0870.2005.00104.x>.
Mishra et al. (2018) <doi:10.1007/s00382-018-4404-z>.
Sanchez-Garcia et al. (2019) <doi:10.5194/asr-16-165-2019>.
Straus et al. (2007) <doi:10.1175/JCLI4070.1>.
Terzago et al. (2018) <doi:10.5194/nhess-18-2825-2018>.
Torralba et al. (2017) <doi:10.1175/JAMC-D-16-0204.1>.
D'Onofrio et al. (2014) <doi:10.1175/JHM-D-13-096.1>.
Verfaillie et al. (2017) <doi:10.5194/gmd-10-4257-2017>.
Van Schaeybroeck et al. (2019) <doi:10.1016/B978-0-12-812372-0.00010-8>.
Yiou et al. (2013) <doi:10.1007/s00382-012-1626-3>.
Author: Nuria Perez-Zanon [aut, cre] (<https://orcid.org/0000-0001-8568-3071>),
Louis-Philippe Caron [aut] (<https://orcid.org/0000-0001-5221-0147>),
Carmen Alvarez-Castro [aut] (<https://orcid.org/0000-0002-9958-010X>),
Lauriane Batte [aut],
Jost von Hardenberg [aut] (<https://orcid.org/0000-0002-5312-8070>),
Llorenç LLedo [aut],
Nicolau Manubens [aut],
Eroteida Sanchez-Garcia [aut],
Bert van Schaeybroeck [aut],
Veronica Torralba [aut],
Deborah Verfaillie [aut],
Filippo Cali Quaglia [ctb],
Maria M. Chaves-Montero [ctb],
Chihchung Chou [ctb],
Nicola Cortesi [ctb],
Susanna Corti [ctb],
Paolo Davini [ctb],
Gildas Dayon [ctb],
Marta Dominguez [ctb],
Federico Fabiano [ctb],
Ignazio Giuntoli [ctb],
Raul Marcos [ctb],
Paola Marson [ctb],
Niti Mishra [ctb],
Jesus Peña [ctb],
Francesc Roura-Adserias [ctb],
Silvia Terzago [ctb],
Danila Volpi [ctb],
BSC-CNS [cph]
Maintainer: Nuria Perez-Zanon <nuria.perez@bsc.es>
Diff between CSTools versions 3.1.0 dated 2020-07-02 and 4.0.0 dated 2021-02-23
CSTools-3.1.0/CSTools/data/areave_data.RData |only CSTools-3.1.0/CSTools/man/areave_data.Rd |only CSTools-4.0.0/CSTools/DESCRIPTION | 27 CSTools-4.0.0/CSTools/MD5 | 220 + CSTools-4.0.0/CSTools/NAMESPACE | 28 CSTools-4.0.0/CSTools/NEWS.md | 33 CSTools-4.0.0/CSTools/R/AnalogsPred_train.R |only CSTools-4.0.0/CSTools/R/CST_AdamontAnalog.R |only CSTools-4.0.0/CSTools/R/CST_AdamontQQCorr.R |only CSTools-4.0.0/CSTools/R/CST_Analogs.R | 1107 ++++++---- CSTools-4.0.0/CSTools/R/CST_AnalogsPredictors.R |only CSTools-4.0.0/CSTools/R/CST_Anomaly.R | 3 CSTools-4.0.0/CSTools/R/CST_BiasCorrection.R | 1 CSTools-4.0.0/CSTools/R/CST_Calibration.R | 298 +- CSTools-4.0.0/CSTools/R/CST_CategoricalEnsCombination.R | 54 CSTools-4.0.0/CSTools/R/CST_Load.R | 2 CSTools-4.0.0/CSTools/R/CST_MergeDims.R | 4 CSTools-4.0.0/CSTools/R/CST_MultiMetric.R | 214 + CSTools-4.0.0/CSTools/R/CST_MultivarRMSE.R | 13 CSTools-4.0.0/CSTools/R/CST_QuantileMapping.R | 120 + CSTools-4.0.0/CSTools/R/CST_RFSlope.R | 28 CSTools-4.0.0/CSTools/R/CST_RFWeights.R | 110 CSTools-4.0.0/CSTools/R/CST_RainFARM.R | 138 - CSTools-4.0.0/CSTools/R/CST_RegimesAssign.R | 14 CSTools-4.0.0/CSTools/R/CST_SaveExp.R | 17 CSTools-4.0.0/CSTools/R/CST_SplitDim.R | 79 CSTools-4.0.0/CSTools/R/CST_WeatherRegimes.R | 4 CSTools-4.0.0/CSTools/R/PlotCombinedMap.R | 2 CSTools-4.0.0/CSTools/R/PlotForecastPDF.R | 194 + CSTools-4.0.0/CSTools/R/PlotMostLikelyQuantileMap.R | 1 CSTools-4.0.0/CSTools/R/PlotPDFsOLE.R | 41 CSTools-4.0.0/CSTools/R/PlotTriangles4Categories.R | 14 CSTools-4.0.0/CSTools/R/sample_data.R | 39 CSTools-4.0.0/CSTools/build/vignette.rds |binary CSTools-4.0.0/CSTools/inst/doc/Analogs_vignette.R |only CSTools-4.0.0/CSTools/inst/doc/Analogs_vignette.Rmd |only CSTools-4.0.0/CSTools/inst/doc/Analogs_vignette.html |only CSTools-4.0.0/CSTools/inst/doc/BestEstimateIndex_vignette.Rmd | 8 CSTools-4.0.0/CSTools/inst/doc/BestEstimateIndex_vignette.html | 8 CSTools-4.0.0/CSTools/inst/doc/Data_Considerations.Rmd |only CSTools-4.0.0/CSTools/inst/doc/Data_Considerations.html |only CSTools-4.0.0/CSTools/inst/doc/ENSclustering_vignette.Rmd | 4 CSTools-4.0.0/CSTools/inst/doc/ENSclustering_vignette.html | 4 CSTools-4.0.0/CSTools/inst/doc/MostLikelyTercile_vignette.Rmd |only CSTools-4.0.0/CSTools/inst/doc/MostLikelyTercile_vignette.html |only CSTools-4.0.0/CSTools/inst/doc/MultiModelSkill_vignette.Rmd | 56 CSTools-4.0.0/CSTools/inst/doc/MultiModelSkill_vignette.html | 59 CSTools-4.0.0/CSTools/inst/doc/MultivarRMSE_vignette.html | 2 CSTools-4.0.0/CSTools/inst/doc/PlotForecastPDF.R | 23 CSTools-4.0.0/CSTools/inst/doc/PlotForecastPDF.Rmd | 47 CSTools-4.0.0/CSTools/inst/doc/PlotForecastPDF.html | 51 CSTools-4.0.0/CSTools/inst/doc/RainFARM_vignette.Rmd | 6 CSTools-4.0.0/CSTools/inst/doc/RainFARM_vignette.html | 6 CSTools-4.0.0/CSTools/inst/doc/WeatherRegimes_vignette.Rmd | 2 CSTools-4.0.0/CSTools/inst/doc/WeatherRegimes_vignette.html | 8 CSTools-4.0.0/CSTools/man/AdamontQQCorr.Rd |only CSTools-4.0.0/CSTools/man/Analogs.Rd | 392 +-- CSTools-4.0.0/CSTools/man/CST_AdamontAnalog.Rd |only CSTools-4.0.0/CSTools/man/CST_AdamontQQCorr.Rd |only CSTools-4.0.0/CSTools/man/CST_Analogs.Rd | 115 - CSTools-4.0.0/CSTools/man/CST_AnalogsPredictors.Rd |only CSTools-4.0.0/CSTools/man/CST_Calibration.Rd | 17 CSTools-4.0.0/CSTools/man/CST_MultiMetric.Rd | 34 CSTools-4.0.0/CSTools/man/CST_MultivarRMSE.Rd | 2 CSTools-4.0.0/CSTools/man/CST_QuantileMapping.Rd | 30 CSTools-4.0.0/CSTools/man/CST_RFSlope.Rd | 4 CSTools-4.0.0/CSTools/man/CST_RFWeights.Rd | 23 CSTools-4.0.0/CSTools/man/CST_RainFARM.Rd | 25 CSTools-4.0.0/CSTools/man/CST_SaveExp.Rd | 2 CSTools-4.0.0/CSTools/man/CST_SplitDim.Rd | 16 CSTools-4.0.0/CSTools/man/Calibration.Rd | 24 CSTools-4.0.0/CSTools/man/CategoricalEnsCombination.Rd |only CSTools-4.0.0/CSTools/man/MultiMetric.Rd |only CSTools-4.0.0/CSTools/man/PlotPDFsOLE.Rd | 21 CSTools-4.0.0/CSTools/man/PlotTriangles4Categories.Rd | 6 CSTools-4.0.0/CSTools/man/QuantileMapping.Rd |only CSTools-4.0.0/CSTools/man/RFSlope.Rd | 11 CSTools-4.0.0/CSTools/man/RF_Weights.Rd |only CSTools-4.0.0/CSTools/man/RainFARM.Rd | 18 CSTools-4.0.0/CSTools/man/SplitDim.Rd | 12 CSTools-4.0.0/CSTools/man/training_analogs.Rd |only CSTools-4.0.0/CSTools/src |only CSTools-4.0.0/CSTools/vignettes/Analogs_vignette.Rmd |only CSTools-4.0.0/CSTools/vignettes/BestEstimateIndex_vignette.Rmd | 8 CSTools-4.0.0/CSTools/vignettes/Data_Considerations.Rmd |only CSTools-4.0.0/CSTools/vignettes/ENSclustering_vignette.Rmd | 4 CSTools-4.0.0/CSTools/vignettes/Figures/Analogs1.png |only CSTools-4.0.0/CSTools/vignettes/Figures/Analogs2.png |only CSTools-4.0.0/CSTools/vignettes/Figures/Analogs3.png |only CSTools-4.0.0/CSTools/vignettes/Figures/Analogs4.png |only CSTools-4.0.0/CSTools/vignettes/Figures/Analogs5.png |only CSTools-4.0.0/CSTools/vignettes/Figures/Analogs6.png |only CSTools-4.0.0/CSTools/vignettes/Figures/BestEstimateIndex_fig1.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/BestEstimateIndex_fig2.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/BestEstimateIndex_fig3.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/BestEstimateIndex_fig4.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/CSTvsNonCST.png |only CSTools-4.0.0/CSTools/vignettes/Figures/EnsClus_4clus_both_mem_std_Fig1.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/EnsClus_4clus_both_mem_std_Fig2.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/Meteofrance_r360x180.png |only CSTools-4.0.0/CSTools/vignettes/Figures/MostLikelyTercile_fig1.png |only CSTools-4.0.0/CSTools/vignettes/Figures/MostLikelyTercile_fig2.png |only CSTools-4.0.0/CSTools/vignettes/Figures/MostLikelyTercile_fig3.png |only CSTools-4.0.0/CSTools/vignettes/Figures/MultiModelSkill_cor_tas_1992-2012.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/MultiModelSkill_rms_tas_1992-2012.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/MultiModelSkill_rmsss_tas_1992-2012.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/MultivarRMSE_gloseas5_tas_prlr_1992-2012.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/Obs_Persistence.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/PlotForecastPDF_ex1.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/PlotForecastPDF_ex2.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/PlotForecastPDF_ex3.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/PlotForecastPDF_ex4.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/RainFARM_fig1.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/RainFARM_fig2.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/observed_regimes.png |binary CSTools-4.0.0/CSTools/vignettes/Figures/predicted_regimes.png |binary CSTools-4.0.0/CSTools/vignettes/MostLikelyTercile_vignette.Rmd |only CSTools-4.0.0/CSTools/vignettes/MultiModelSkill_vignette.Rmd | 56 CSTools-4.0.0/CSTools/vignettes/PlotForecastPDF.Rmd | 47 CSTools-4.0.0/CSTools/vignettes/RainFARM_vignette.Rmd | 6 CSTools-4.0.0/CSTools/vignettes/WeatherRegimes_vignette.Rmd | 2 121 files changed, 2504 insertions(+), 1460 deletions(-)
Title: Tabular Data Backed by Partitioned 'fst' Files
Description: Intended for larger-than-memory tabular data, 'prt' objects provide an interface to read row and/or column subsets into memory as data.table objects. Data queries, constructed as 'R' expressions, are evaluated using the non-standard evaluation framework provided by 'rlang' and file-backing is powered by the fast and efficient 'fst' package.
Author: Nicolas Bennett [aut, cre],
Drago Plecko [ctb]
Maintainer: Nicolas Bennett <nicolas.bennett@stat.math.ethz.ch>
Diff between prt versions 0.1.2 dated 2020-09-29 and 0.1.3 dated 2021-02-23
DESCRIPTION | 6 MD5 | 36 ++-- NAMESPACE | 3 NEWS.md | 4 R/format.R | 79 +++++----- R/utils.R | 12 - README.md | 14 - build/vignette.rds |binary inst/doc/prt.R | 5 inst/doc/prt.Rmd | 6 inst/doc/prt.html | 185 +++++++++++++----------- tests/testthat/output/format/POSIXct-8-60.txt | 18 +- tests/testthat/output/format/iris--70.txt | 12 - tests/testthat/output/format/iris-5-30.txt | 12 - tests/testthat/output/format/iris-inf-30.txt | 198 +++++++++++++------------- tests/testthat/output/format/iris-neg-30.txt | 12 - tests/testthat/output/format/long-5-30.txt | 20 +- tests/testthat/output/format/mtcars-8-30.txt | 18 +- vignettes/prt.Rmd | 6 19 files changed, 336 insertions(+), 310 deletions(-)
Title: Statistical Methods for Analysing Multivariate Abundance Data
Description: A set of tools for displaying, modeling and analysing
multivariate abundance data in community ecology. See
'mvabund-package.Rd' for details of overall package organization.
The package is implemented with the Gnu Scientific Library
(<http://www.gnu.org/software/gsl/>) and 'Rcpp'
(<http://dirk.eddelbuettel.com/code/rcpp.html>) 'R' / 'C++' classes.
Author: Yi Wang [aut],
Ulrike Naumann [aut],
Dirk Eddelbuettel [aut],
John Wilshire [aut],
David Warton [aut, cre],
Julian Byrnes [ctb],
Ralph dos Santos Silva [ctb, cph],
Jenni Niku [ctb],
Ian Renner [ctb],
Stephen Wright [ctb]
Maintainer: David Warton <David.Warton@unsw.edu.au>
Diff between mvabund versions 4.1.6 dated 2020-12-18 and 4.1.9 dated 2021-02-23
DESCRIPTION | 8 ++++---- MD5 | 14 +++++++------- R/best.r.sq.R | 6 ++++-- R/coefplot.manyglm.R | 4 ++-- R/default.plot.manyglm.R | 12 +++++++----- R/default.plot.manylm.R | 29 +++++++++++++++++++---------- R/residuals.manyglm.R | 1 + README.md | 4 ++-- 8 files changed, 46 insertions(+), 32 deletions(-)
Title: Interface to the Search API for 'PLoS' Journals
Description: A programmatic interface to the 'SOLR' based
search API (<http://api.plos.org/>) provided by the Public
Library of Science journals to search their articles.
Functions are included for searching for articles, retrieving
articles, making plots, doing 'faceted' searches,
'highlight' searches, and viewing results of 'highlighted'
searches in a browser.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Carl Boettiger [aut],
Karthik Ram [aut],
rOpenSci [fnd] (https://ropensci.org)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between rplos versions 0.9.0 dated 2020-04-08 and 1.0.0 dated 2021-02-23
rplos-0.9.0/rplos/README.md |only rplos-1.0.0/rplos/DESCRIPTION | 19 rplos-1.0.0/rplos/LICENSE | 2 rplos-1.0.0/rplos/MD5 | 82 rplos-1.0.0/rplos/NEWS.md | 8 rplos-1.0.0/rplos/R/plossubject.R | 2 rplos-1.0.0/rplos/R/rplos-package.R | 2 rplos-1.0.0/rplos/build/vignette.rds |binary rplos-1.0.0/rplos/inst/doc/facethighlight.Rmd | 36 rplos-1.0.0/rplos/inst/doc/facethighlight.html | 73 rplos-1.0.0/rplos/inst/doc/fulltext.Rmd | 64 rplos-1.0.0/rplos/inst/doc/fulltext.html | 103 rplos-1.0.0/rplos/inst/doc/rplos.Rmd | 84 rplos-1.0.0/rplos/inst/doc/rplos.html | 125 rplos-1.0.0/rplos/man/figures/plosword1plot-1.png |binary rplos-1.0.0/rplos/man/figures/throughtime1-1.png |binary rplos-1.0.0/rplos/man/figures/unnamed-chunk-21-1.png |binary rplos-1.0.0/rplos/man/highplos.Rd | 2 rplos-1.0.0/rplos/man/plossubject.Rd | 2 rplos-1.0.0/rplos/man/rplos.Rd | 2 rplos-1.0.0/rplos/tests/fixtures/full_text_urls_all_journals.yml |12439 ---------- rplos-1.0.0/rplos/tests/fixtures/plosfigtabcaps_id.yml |only rplos-1.0.0/rplos/tests/testthat/test-facetplos.R | 4 rplos-1.0.0/rplos/tests/testthat/test-formatarticleurl.R | 4 rplos-1.0.0/rplos/tests/testthat/test-fulltext.R | 12 rplos-1.0.0/rplos/tests/testthat/test-highbrow.R | 4 rplos-1.0.0/rplos/tests/testthat/test-highplos.R | 4 rplos-1.0.0/rplos/tests/testthat/test-journalnamekey.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plosabstract.R | 3 rplos-1.0.0/rplos/tests/testthat/test-plosauthor.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plosfields.R | 7 rplos-1.0.0/rplos/tests/testthat/test-plosfigtabcaps.R | 8 rplos-1.0.0/rplos/tests/testthat/test-plossubject.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plostitle.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plosviews.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plosword.R | 4 rplos-1.0.0/rplos/tests/testthat/test-plot_throughtime.R | 3 rplos-1.0.0/rplos/tests/testthat/test-searchplos.R | 6 rplos-1.0.0/rplos/vignettes/facethighlight.Rmd | 36 rplos-1.0.0/rplos/vignettes/fulltext.Rmd | 64 rplos-1.0.0/rplos/vignettes/fulltext.Rmd.og | 6 rplos-1.0.0/rplos/vignettes/rplos.Rmd | 84 rplos-1.0.0/rplos/vignettes/rplos.Rmd.og | 2 43 files changed, 602 insertions(+), 12714 deletions(-)
Title: Mosaic Plots in the 'ggplot2' Framework
Description: Mosaic plots in the 'ggplot2' framework. Mosaic
plot functionality is provided in a single 'ggplot2' layer by calling
the geom 'mosaic'.
Author: Haley Jeppson [aut, cre],
Heike Hofmann [aut],
Di Cook [aut],
Hadley Wickham [ctb]
Maintainer: Haley Jeppson <hjeppson@iastate.edu>
Diff between ggmosaic versions 0.2.0 dated 2018-09-12 and 0.3.3 dated 2021-02-23
ggmosaic-0.2.0/ggmosaic/man/scale_type.product.Rd |only ggmosaic-0.2.0/ggmosaic/man/scale_type.tbl_df.Rd |only ggmosaic-0.3.3/ggmosaic/DESCRIPTION | 18 ggmosaic-0.3.3/ggmosaic/MD5 | 65 - ggmosaic-0.3.3/ggmosaic/NAMESPACE | 21 ggmosaic-0.3.3/ggmosaic/NEWS.md | 16 ggmosaic-0.3.3/ggmosaic/R/calculate.R | 12 ggmosaic-0.3.3/ggmosaic/R/data.R | 88 + ggmosaic-0.3.3/ggmosaic/R/geom-mosaic-jitter.R |only ggmosaic-0.3.3/ggmosaic/R/geom-mosaic-text.R |only ggmosaic-0.3.3/ggmosaic/R/geom-mosaic.r | 91 + ggmosaic-0.3.3/ggmosaic/R/scale-product.R | 73 - ggmosaic-0.3.3/ggmosaic/R/stat-mosaic-jitter.r |only ggmosaic-0.3.3/ggmosaic/R/stat-mosaic-text.R |only ggmosaic-0.3.3/ggmosaic/R/stat-mosaic.r | 135 +- ggmosaic-0.3.3/ggmosaic/R/theme-mosaic.R |only ggmosaic-0.3.3/ggmosaic/README.md | 61 - ggmosaic-0.3.3/ggmosaic/build/vignette.rds |binary ggmosaic-0.3.3/ggmosaic/data/fly.rda |binary ggmosaic-0.3.3/ggmosaic/data/happy.rda |binary ggmosaic-0.3.3/ggmosaic/data/titanic.rda |only ggmosaic-0.3.3/ggmosaic/inst/doc/ggmosaic.R | 354 +++---- ggmosaic-0.3.3/ggmosaic/inst/doc/ggmosaic.Rmd | 445 ++++---- ggmosaic-0.3.3/ggmosaic/inst/doc/ggmosaic.html | 750 +++++++-------- ggmosaic-0.3.3/ggmosaic/inst/server.R | 2 ggmosaic-0.3.3/ggmosaic/man/GeomMosaic.Rd |only ggmosaic-0.3.3/ggmosaic/man/GeomMosaicJitter.Rd |only ggmosaic-0.3.3/ggmosaic/man/GeomMosaicText.Rd |only ggmosaic-0.3.3/ggmosaic/man/StatMosaicJitter.Rd |only ggmosaic-0.3.3/ggmosaic/man/StatMosaicText.Rd |only ggmosaic-0.3.3/ggmosaic/man/figures/README-example-1.png |binary ggmosaic-0.3.3/ggmosaic/man/fly.Rd | 60 - ggmosaic-0.3.3/ggmosaic/man/geom_mosaic.Rd | 108 +- ggmosaic-0.3.3/ggmosaic/man/geom_mosaic_jitter.Rd |only ggmosaic-0.3.3/ggmosaic/man/geom_mosaic_text.Rd |only ggmosaic-0.3.3/ggmosaic/man/happy.Rd | 30 ggmosaic-0.3.3/ggmosaic/man/prodcalc.Rd | 11 ggmosaic-0.3.3/ggmosaic/man/product.Rd | 17 ggmosaic-0.3.3/ggmosaic/man/scale_x_productlist.Rd | 98 + ggmosaic-0.3.3/ggmosaic/man/theme_mosaic.Rd |only ggmosaic-0.3.3/ggmosaic/man/titanic.Rd |only ggmosaic-0.3.3/ggmosaic/vignettes/ggmosaic.Rmd | 445 ++++---- 42 files changed, 1527 insertions(+), 1373 deletions(-)
Title: Data Management of Large Hierarchical Data
Description: Import 'SPSS' data, handle and change 'SPSS' meta data, store and access large hierarchical data in 'SQLite' data bases.
Author: Benjamin Becker [aut, cre]
Maintainer: Benjamin Becker <b.becker@iqb.hu-berlin.de>
Diff between eatGADS versions 0.15.2 dated 2020-11-25 and 0.16.0 dated 2021-02-23
eatGADS-0.15.2/eatGADS/tests/testthat/test_writeSPSS.R |only eatGADS-0.16.0/eatGADS/DESCRIPTION | 9 eatGADS-0.16.0/eatGADS/MD5 | 117 - eatGADS-0.16.0/eatGADS/NAMESPACE | 13 eatGADS-0.16.0/eatGADS/NEWS.md | 29 eatGADS-0.16.0/eatGADS/R/GADSdat_utilities.R | 9 eatGADS-0.16.0/eatGADS/R/applyChangeMeta.R | 157 + eatGADS-0.16.0/eatGADS/R/changeSPSSformat.R | 19 eatGADS-0.16.0/eatGADS/R/changeValLabels.R | 6 eatGADS-0.16.0/eatGADS/R/checkMissings.R | 2 eatGADS-0.16.0/eatGADS/R/checkValLabels.R |only eatGADS-0.16.0/eatGADS/R/checkValue.R | 38 eatGADS-0.16.0/eatGADS/R/collapseColumns.R | 12 eatGADS-0.16.0/eatGADS/R/compareGADS.R |only eatGADS-0.16.0/eatGADS/R/extract_labels.R | 3 eatGADS-0.16.0/eatGADS/R/getChangeMeta.R | 5 eatGADS-0.16.0/eatGADS/R/import_stata.R |only eatGADS-0.16.0/eatGADS/R/recode2NA.R |only eatGADS-0.16.0/eatGADS/R/recodeGADS.R | 67 eatGADS-0.16.0/eatGADS/R/recodeString2NA.R | 39 eatGADS-0.16.0/eatGADS/R/removeValLabels.R | 37 eatGADS-0.16.0/eatGADS/R/write_spss.R | 37 eatGADS-0.16.0/eatGADS/README.md | 16 eatGADS-0.16.0/eatGADS/build/partial.rdb |binary eatGADS-0.16.0/eatGADS/inst/doc/createGADS.html | 474 +---- eatGADS-0.16.0/eatGADS/inst/doc/getGADS.html | 498 +---- eatGADS-0.16.0/eatGADS/inst/doc/import_raw.html | 608 ++----- eatGADS-0.16.0/eatGADS/inst/doc/import_spss.html | 414 +--- eatGADS-0.16.0/eatGADS/inst/doc/recoding_forcedChoice.R | 6 eatGADS-0.16.0/eatGADS/inst/doc/recoding_forcedChoice.html | 592 ++---- eatGADS-0.16.0/eatGADS/inst/doc/recoding_forcedChoice.rmd | 8 eatGADS-0.16.0/eatGADS/inst/doc/recoding_multipleChoice.html | 857 +++------- eatGADS-0.16.0/eatGADS/man/applyChangeMeta.Rd | 23 eatGADS-0.16.0/eatGADS/man/changeValLabels.Rd | 6 eatGADS-0.16.0/eatGADS/man/checkEmptyValLabels.Rd |only eatGADS-0.16.0/eatGADS/man/checkMissings.Rd | 2 eatGADS-0.16.0/eatGADS/man/checkValue.Rd | 17 eatGADS-0.16.0/eatGADS/man/collapseColumns.Rd | 4 eatGADS-0.16.0/eatGADS/man/compareGADS.Rd |only eatGADS-0.16.0/eatGADS/man/import_stata.Rd |only eatGADS-0.16.0/eatGADS/man/recode2NA.Rd |only eatGADS-0.16.0/eatGADS/man/recodeGADS.Rd | 31 eatGADS-0.16.0/eatGADS/man/recodeString2NA.Rd | 21 eatGADS-0.16.0/eatGADS/man/removeValLabels.Rd | 25 eatGADS-0.16.0/eatGADS/man/write_spss.Rd | 25 eatGADS-0.16.0/eatGADS/tests/testthat/helper_spss_datetime.sav |only eatGADS-0.16.0/eatGADS/tests/testthat/test_GADSdat_utilities.R | 10 eatGADS-0.16.0/eatGADS/tests/testthat/test_applyChangeMeta.R | 106 + eatGADS-0.16.0/eatGADS/tests/testthat/test_changeMissings.R | 109 - eatGADS-0.16.0/eatGADS/tests/testthat/test_changeSPSSformat.R | 10 eatGADS-0.16.0/eatGADS/tests/testthat/test_changeValLabels.R | 5 eatGADS-0.16.0/eatGADS/tests/testthat/test_checkValLabels.R |only eatGADS-0.16.0/eatGADS/tests/testthat/test_checkValue.R | 65 eatGADS-0.16.0/eatGADS/tests/testthat/test_collapseColumns.R | 10 eatGADS-0.16.0/eatGADS/tests/testthat/test_collapseMC_Text.R | 8 eatGADS-0.16.0/eatGADS/tests/testthat/test_compareGADS.R |only eatGADS-0.16.0/eatGADS/tests/testthat/test_getChangeMeta.R | 12 eatGADS-0.16.0/eatGADS/tests/testthat/test_import_raw.R | 3 eatGADS-0.16.0/eatGADS/tests/testthat/test_recode2NA.R |only eatGADS-0.16.0/eatGADS/tests/testthat/test_recodeGADS.R | 27 eatGADS-0.16.0/eatGADS/tests/testthat/test_recodeString2NA.R | 32 eatGADS-0.16.0/eatGADS/tests/testthat/test_remove2NAchar.R | 3 eatGADS-0.16.0/eatGADS/tests/testthat/test_removeValLabels.R | 26 eatGADS-0.16.0/eatGADS/tests/testthat/test_times2character.R | 15 eatGADS-0.16.0/eatGADS/tests/testthat/test_write_spss.R |only eatGADS-0.16.0/eatGADS/tests/testthat/test_write_stata.R |only eatGADS-0.16.0/eatGADS/vignettes/recoding_forcedChoice.rmd | 8 67 files changed, 1943 insertions(+), 2732 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-06-09 2.3.2
2020-03-22 2.2.4.1
2019-03-25 2.2.4
2019-01-07 2.2.3
2018-08-01 2.2.2
2016-04-22 2.2.1.11
2015-12-22 2.2.1.7
2015-11-07 2.2.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-11-03 1.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-04-21 1.2
2016-07-19 1.0
2014-05-30 0.1-18
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-02-24 1.55
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-12-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-07 0.1.5
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2016-11-06 0.1.14
Title: Reproduce Statistical Analyses and Meta-Analyses
Description: Includes data analysis functions (e.g., to calculate effect sizes and 95% Confidence Intervals (CI) on Standardised Effect Sizes (d) for AB/BA cross-over repeated-measures experimental designs), data presentation functions (e.g., density curve overlaid on histogram), and the data sets analyzed in different research papers in software engineering (e.g., related to software defect prediction or multi-site experiment concerning the extent to which structured abstracts were clearer and more complete than conventional abstracts) to streamline reproducible research in software engineering.
Author: Lech Madeyski [cre, aut, ctb] (The main contributor and maintainer),
Barbara Kitchenham [ctb] (Data and code contributor),
Tomasz Lewowski [ctb] (Data and code contributor),
Marian Jureczko [ctb] (Data contributor),
David Budgen [ctb] (Data contributor),
Pearl Brereton [ctb] (Data contributor),
Jacky Keung [ctb] (Data contributor),
Stuart Charters [ctb] (Data contributor),
Shirley Gibbs [ctb] (Data contributor),
Amnart Pohthong [ctb] (Data contributor),
Giuseppe Scanniello [ctb] (Data contributor),
Carmine Gravino [ctb] (Data contributor)
Maintainer: Lech Madeyski <lech.madeyski@gmail.com>
Diff between reproducer versions 0.4.1 dated 2021-02-14 and 0.4.2 dated 2021-02-23
reproducer-0.4.1/reproducer/man/simulateRandomzedDesignEffectSizes.Rd |only reproducer-0.4.2/reproducer/DESCRIPTION | 8 ++--- reproducer-0.4.2/reproducer/MD5 | 12 ++++---- reproducer-0.4.2/reproducer/NAMESPACE | 2 - reproducer-0.4.2/reproducer/NEWS.md | 6 ++++ reproducer-0.4.2/reproducer/R/NPSimulation.R | 14 +++++----- reproducer-0.4.2/reproducer/man/RandomizedBlocksExperimentSimulations.Rd | 6 +--- reproducer-0.4.2/reproducer/man/simulateRandomizedDesignEffectSizes.Rd |only 8 files changed, 26 insertions(+), 22 deletions(-)
Title: Kriging Methods for Computer Experiments
Description: Estimation, validation and prediction of kriging models. Important functions : km, print.km, plot.km, predict.km.
Author: Olivier Roustant, David Ginsbourger, Yves Deville. Contributors: Clement Chevalier, Yann Richet.
Maintainer: Olivier Roustant <roustant@insa-toulouse.fr>
Diff between DiceKriging versions 1.5.8 dated 2020-11-05 and 1.6.0 dated 2021-02-23
CHANGELOG | 12 ++++++++++++ DESCRIPTION | 8 ++++---- MD5 | 13 ++++++++----- NAMESPACE | 1 + R/cv.R |only man/DiceKriging-package.Rd | 4 ++-- man/cv.Rd |only man/leaveOneOut.km.Rd | 7 +++++-- tests/testthat/tests-cv.R |only 9 files changed, 32 insertions(+), 13 deletions(-)
Title: Bayesian Object Oriented Modeling
Description: A C++ library for Bayesian modeling, with an emphasis on Markov
chain Monte Carlo. Although boom contains a few R utilities (mainly plotting
functions), its primary purpose is to install the BOOM C++ library on your
system so that other packages can link against it.
Author: Steven L. Scott is the sole author and creator of the BOOM project.
Some code in the BOOM libraries has been modified from other open source
projects. These include Cephes (obtained from Netlib, written by Stephen
L. Moshier), NEWUOA (M.J.D Powell, obtained from Powell's web site), and a
modified version of the R math libraries (R core development team). Original
copyright notices have been maintained in all source files. In these cases,
copyright claimed by Steven L. Scott is limited to modifications made to the
original code. Google claims copyright for code written while Steven
L. Scott was employed at Google from 2008 - 2018, but BOOM is not an
officially supported Google project.
Maintainer: Steven L. Scott <steve.the.bayesian@gmail.com>
Diff between Boom versions 0.9.6 dated 2020-04-30 and 0.9.7 dated 2021-02-23
DESCRIPTION | 8 MD5 | 462 +++--- inst/include/Bmath/Bmath.hpp | 1 inst/include/Bmath/bessel.hpp |only inst/include/Eigen/CMakeLists.txt |only inst/include/Eigen/Cholesky | 5 inst/include/Eigen/Core | 34 inst/include/Eigen/Eigenvalues | 8 inst/include/Eigen/Geometry | 4 inst/include/Eigen/LU | 4 inst/include/Eigen/QR | 8 inst/include/Eigen/QtAlignedMalloc | 2 inst/include/Eigen/SVD | 4 inst/include/Eigen/SparseQR | 1 inst/include/Eigen/src/Cholesky/LDLT.h | 14 inst/include/Eigen/src/Cholesky/LLT.h | 26 inst/include/Eigen/src/Core/Array.h | 2 inst/include/Eigen/src/Core/ArrayBase.h | 4 inst/include/Eigen/src/Core/AssignEvaluator.h | 66 inst/include/Eigen/src/Core/Assign_MKL.h | 6 inst/include/Eigen/src/Core/ConditionEstimator.h | 2 inst/include/Eigen/src/Core/CoreEvaluators.h | 39 inst/include/Eigen/src/Core/CwiseUnaryView.h | 2 inst/include/Eigen/src/Core/DenseBase.h | 7 inst/include/Eigen/src/Core/DenseStorage.h | 6 inst/include/Eigen/src/Core/Diagonal.h | 5 inst/include/Eigen/src/Core/Dot.h | 17 inst/include/Eigen/src/Core/GeneralProduct.h | 21 inst/include/Eigen/src/Core/GenericPacketMath.h | 9 inst/include/Eigen/src/Core/Map.h | 17 inst/include/Eigen/src/Core/MapBase.h | 11 inst/include/Eigen/src/Core/MathFunctions.h | 80 - inst/include/Eigen/src/Core/MathFunctionsImpl.h | 23 inst/include/Eigen/src/Core/Matrix.h | 2 inst/include/Eigen/src/Core/MatrixBase.h | 38 inst/include/Eigen/src/Core/PermutationMatrix.h | 28 inst/include/Eigen/src/Core/PlainObjectBase.h | 16 inst/include/Eigen/src/Core/Product.h | 10 inst/include/Eigen/src/Core/ProductEvaluators.h | 59 inst/include/Eigen/src/Core/Redux.h | 2 inst/include/Eigen/src/Core/Ref.h | 7 inst/include/Eigen/src/Core/SelfAdjointView.h | 6 inst/include/Eigen/src/Core/SelfCwiseBinaryOp.h | 4 inst/include/Eigen/src/Core/SolveTriangular.h | 9 inst/include/Eigen/src/Core/StableNorm.h | 2 inst/include/Eigen/src/Core/Transpose.h | 2 inst/include/Eigen/src/Core/Transpositions.h | 41 inst/include/Eigen/src/Core/TriangularMatrix.h | 8 inst/include/Eigen/src/Core/arch/AVX/Complex.h | 36 inst/include/Eigen/src/Core/arch/AVX/PacketMath.h | 24 inst/include/Eigen/src/Core/arch/AVX512/MathFunctions.h | 95 - inst/include/Eigen/src/Core/arch/AVX512/PacketMath.h | 729 ++++------ inst/include/Eigen/src/Core/arch/AltiVec/Complex.h | 35 inst/include/Eigen/src/Core/arch/AltiVec/PacketMath.h | 46 inst/include/Eigen/src/Core/arch/CUDA/Half.h | 254 ++- inst/include/Eigen/src/Core/arch/CUDA/PacketMathHalf.h | 9 inst/include/Eigen/src/Core/arch/Default/ConjHelper.h |only inst/include/Eigen/src/Core/arch/NEON/Complex.h | 12 inst/include/Eigen/src/Core/arch/NEON/PacketMath.h | 31 inst/include/Eigen/src/Core/arch/SSE/Complex.h | 40 inst/include/Eigen/src/Core/arch/SSE/PacketMath.h | 24 inst/include/Eigen/src/Core/arch/SSE/TypeCasting.h | 28 inst/include/Eigen/src/Core/arch/ZVector/Complex.h | 3 inst/include/Eigen/src/Core/functors/BinaryFunctors.h | 25 inst/include/Eigen/src/Core/functors/StlFunctors.h | 4 inst/include/Eigen/src/Core/functors/UnaryFunctors.h | 2 inst/include/Eigen/src/Core/products/GeneralBlockPanelKernel.h | 22 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix.h | 37 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular.h | 68 inst/include/Eigen/src/Core/products/GeneralMatrixMatrixTriangular_BLAS.h | 20 inst/include/Eigen/src/Core/products/GeneralMatrixMatrix_BLAS.h | 25 inst/include/Eigen/src/Core/products/GeneralMatrixVector.h | 8 inst/include/Eigen/src/Core/products/GeneralMatrixVector_BLAS.h | 19 inst/include/Eigen/src/Core/products/Parallelizer.h | 9 inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix.h | 54 inst/include/Eigen/src/Core/products/SelfadjointMatrixMatrix_BLAS.h | 72 inst/include/Eigen/src/Core/products/SelfadjointMatrixVector_BLAS.h | 9 inst/include/Eigen/src/Core/products/SelfadjointProduct.h | 4 inst/include/Eigen/src/Core/products/TriangularMatrixMatrix.h | 89 - inst/include/Eigen/src/Core/products/TriangularMatrixMatrix_BLAS.h | 65 inst/include/Eigen/src/Core/products/TriangularMatrixVector.h | 22 inst/include/Eigen/src/Core/products/TriangularMatrixVector_BLAS.h | 46 inst/include/Eigen/src/Core/products/TriangularSolverMatrix.h | 62 inst/include/Eigen/src/Core/products/TriangularSolverMatrix_BLAS.h | 52 inst/include/Eigen/src/Core/util/BlasUtil.h | 115 + inst/include/Eigen/src/Core/util/DisableStupidWarnings.h | 27 inst/include/Eigen/src/Core/util/ForwardDeclarations.h | 6 inst/include/Eigen/src/Core/util/MKL_support.h | 10 inst/include/Eigen/src/Core/util/Macros.h | 75 - inst/include/Eigen/src/Core/util/Memory.h | 24 inst/include/Eigen/src/Core/util/Meta.h | 76 + inst/include/Eigen/src/Core/util/ReenableStupidWarnings.h | 8 inst/include/Eigen/src/Core/util/StaticAssert.h | 120 - inst/include/Eigen/src/Core/util/XprHelper.h | 17 inst/include/Eigen/src/Eigenvalues/ComplexSchur.h | 9 inst/include/Eigen/src/Eigenvalues/GeneralizedEigenSolver.h | 5 inst/include/Eigen/src/Eigenvalues/MatrixBaseEigenvalues.h | 2 inst/include/Eigen/src/Eigenvalues/RealSchur.h | 19 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver.h | 7 inst/include/Eigen/src/Eigenvalues/SelfAdjointEigenSolver_LAPACKE.h | 25 inst/include/Eigen/src/Geometry/AngleAxis.h | 2 inst/include/Eigen/src/Geometry/Quaternion.h | 51 inst/include/Eigen/src/Geometry/Scaling.h | 2 inst/include/Eigen/src/Geometry/Transform.h | 4 inst/include/Eigen/src/Geometry/Translation.h | 6 inst/include/Eigen/src/Geometry/Umeyama.h | 2 inst/include/Eigen/src/IterativeLinearSolvers/BasicPreconditioners.h | 2 inst/include/Eigen/src/IterativeLinearSolvers/ConjugateGradient.h | 5 inst/include/Eigen/src/Jacobi/Jacobi.h | 253 +-- inst/include/Eigen/src/LU/InverseImpl.h | 2 inst/include/Eigen/src/LU/PartialPivLU.h | 5 inst/include/Eigen/src/LU/arch/Inverse_SSE.h | 4 inst/include/Eigen/src/PaStiXSupport/PaStiXSupport.h | 8 inst/include/Eigen/src/PardisoSupport/PardisoSupport.h | 3 inst/include/Eigen/src/SVD/BDCSVD.h | 94 - inst/include/Eigen/src/SVD/JacobiSVD_LAPACKE.h | 5 inst/include/Eigen/src/SVD/SVDBase.h | 4 inst/include/Eigen/src/SparseCholesky/SimplicialCholesky.h | 2 inst/include/Eigen/src/SparseCholesky/SimplicialCholesky_impl.h | 2 inst/include/Eigen/src/SparseCore/AmbiVector.h | 7 inst/include/Eigen/src/SparseCore/ConservativeSparseSparseProduct.h | 67 inst/include/Eigen/src/SparseCore/SparseCwiseUnaryOp.h | 2 inst/include/Eigen/src/SparseCore/SparseMatrix.h | 9 inst/include/Eigen/src/SparseCore/SparseSelfAdjointView.h | 12 inst/include/Eigen/src/SparseCore/SparseSparseProductWithPruning.h | 22 inst/include/Eigen/src/SparseCore/SparseView.h | 1 inst/include/Eigen/src/SparseLU/SparseLU.h | 6 inst/include/Eigen/src/SparseQR/SparseQR.h | 26 inst/include/Eigen/src/StlSupport/StdDeque.h | 6 inst/include/Eigen/src/SuperLUSupport/SuperLUSupport.h | 4 inst/include/Eigen/src/plugins/ArrayCwiseBinaryOps.h | 2 inst/include/LinAlg/Array.hpp | 16 inst/include/LinAlg/Matrix.hpp | 26 inst/include/LinAlg/SWEEP.hpp | 15 inst/include/Models/CategoricalData.hpp | 28 inst/include/Models/DataTypes.hpp | 24 inst/include/Models/FiniteMixtureModel.hpp | 5 inst/include/Models/Glm/GlmCoefs.hpp | 12 inst/include/Models/Glm/LoglinearModel.hpp |only inst/include/Models/Glm/MultivariateRegression.hpp | 14 inst/include/Models/Glm/MvtRegModel.hpp | 4 inst/include/Models/Glm/PosteriorSamplers/LoglinearModelBipfSampler.hpp |only inst/include/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.hpp | 5 inst/include/Models/Glm/RegressionModel.hpp | 6 inst/include/Models/Glm/TRegression.hpp | 6 inst/include/Models/Glm/VariableSelectionPrior.hpp | 4 inst/include/Models/IRT/Item.hpp | 9 inst/include/Models/IRT/PartialCreditModel.hpp | 4 inst/include/Models/Impute |only inst/include/Models/ModelTypes.hpp | 18 inst/include/Models/MultinomialModel.hpp | 27 inst/include/Models/ParamTypes.hpp | 20 inst/include/Models/PointProcess/PoissonProcess.hpp | 14 inst/include/Models/PoissonModel.hpp | 2 inst/include/Models/Policies/CompositeParamPolicy.hpp | 8 inst/include/Models/Policies/IID_DataPolicy.hpp | 17 inst/include/Models/Policies/ManyParamPolicy.hpp | 8 inst/include/Models/Policies/NullParamPolicy.hpp | 4 inst/include/Models/Policies/NullPriorPolicy.hpp | 1 inst/include/Models/Policies/ParamPolicy_1.hpp | 30 inst/include/Models/Policies/ParamPolicy_2.hpp | 54 inst/include/Models/Policies/ParamPolicy_3.hpp | 13 inst/include/Models/Policies/ParamPolicy_4.hpp | 8 inst/include/Models/Policies/PriorPolicy.hpp | 2 inst/include/Models/PosteriorSamplers/MultinomialDirichletSampler.hpp | 27 inst/include/Models/SpdParams.hpp | 2 inst/include/Models/StateSpace/DynamicRegression.hpp | 8 inst/include/Models/StateSpace/StateModels/SemilocalLinearTrend.hpp | 5 inst/include/Models/StateSpace/StateModels/StaticInterceptStateModel.hpp | 9 inst/include/Models/StateSpace/StateSpaceModelBase.hpp | 6 inst/include/Models/WishartModel.hpp | 2 inst/include/TargetFun/Loglike.hpp | 2 inst/include/cpputil/ParamHolder.hpp | 9 inst/include/cpputil/ToString.hpp | 13 inst/include/distributions.hpp | 23 inst/include/distributions/Rmath_dist.hpp | 2 inst/include/distributions/rng.hpp | 14 inst/include/numopt/Integral.hpp | 16 inst/include/r_interface/boom_r_tools.hpp | 20 inst/include/stats/DataTable.hpp | 289 +++ inst/include/stats/ECDF.hpp | 16 inst/include/stats/Encoders.hpp |only inst/include/stats/FreqDist.hpp | 7 inst/include/stats/IQagent.hpp | 33 inst/include/stats/hexbin.hpp |only inst/include/stats/summary.hpp | 113 + src/Bmath/Bmath.hpp | 1 src/Bmath/bessel.hpp |only src/Bmath/bessel_k.cpp |only src/LinAlg/Array.cpp | 74 - src/LinAlg/CorrelationMatrix.cpp | 8 src/LinAlg/Matrix.cpp | 132 + src/LinAlg/SWEEP.cpp | 69 src/LinAlg/Vector.cpp | 28 src/LinAlg/VectorView.cpp | 17 src/Models/CategoricalData.cpp | 29 src/Models/DataTypes.cpp | 28 src/Models/FiniteMixtureModel.cpp | 21 src/Models/Glm/GlmCoefs.cpp | 5 src/Models/Glm/LoglinearModel.cpp |only src/Models/Glm/MultivariateRegression.cpp | 18 src/Models/Glm/MvtRegModel.cpp | 6 src/Models/Glm/PosteriorSamplers/LoglinearModelBipfSampler.cpp |only src/Models/Glm/PosteriorSamplers/MultivariateRegressionSampler.cpp | 11 src/Models/Glm/RegressionModel.cpp | 4 src/Models/Glm/TRegression.cpp | 7 src/Models/Glm/VariableSelectionPrior.cpp | 16 src/Models/IRT/DafePcrItemSampler.cpp | 2 src/Models/IRT/PartialCreditModel.cpp | 4 src/Models/Impute |only src/Models/Mixtures/PosteriorSamplers/SplitMerge.cpp | 43 src/Models/ModelTypes.cpp | 6 src/Models/MultinomialModel.cpp | 55 src/Models/ParamTypes.cpp | 9 src/Models/PoissonModel.cpp | 2 src/Models/Policies/CompositeParamPolicy.cpp | 8 src/Models/Policies/NullParamPolicy.cpp | 10 src/Models/PosteriorSamplers/MultinomialDirichletSampler.cpp | 62 src/Models/SpdParams.cpp | 4 src/Models/StateSpace/PosteriorSamplers/DynamicRegressionDirectGibbs.cpp | 4 src/Models/StateSpace/StateSpaceModelBase.cpp | 4 src/Models/TimeSeries/ArModel.cpp | 1 src/Models/TimeSeries/PosteriorSamplers/NonzeroMeanAr1Sampler.cpp | 6 src/Models/WishartModel.cpp | 2 src/boom_r_tools.cpp | 31 src/cpputil/ParamHolder.cpp | 6 src/distributions/Rmath_dist.cpp | 4 src/distributions/gig.cpp |only src/distributions/mvn.cpp | 18 src/distributions/rng.cpp | 12 src/distributions/trun_gamma.cpp | 6 src/stats/DataTable.cpp | 654 ++++++-- src/stats/ECDF.cpp | 28 src/stats/Encoders.cpp |only src/stats/FreqDist.cpp | 4 src/stats/IQagent.cpp | 48 src/stats/hexbin.cpp |only src/stats/summary.cpp | 133 + 238 files changed, 4459 insertions(+), 2578 deletions(-)
Title: Most Likely Transformations: Documentation and Regression Tests
Description: Additional documentation, a package vignette and
regression tests for package mlt.
Author: Torsten Hothorn [aut, cre] (<https://orcid.org/0000-0001-8301-0471>)
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>
Diff between mlt.docreg versions 1.0-9 dated 2020-12-15 and 1.0-10 dated 2021-02-23
DESCRIPTION | 8 ++--- MD5 | 20 ++++++------ build/vignette.rds |binary inst/NEWS.Rd | 7 ++++ inst/doc/mlt.R | 62 ++++++++++++++++++++++++++++++++++++--- inst/doc/mlt.Rnw | 66 ++++++++++++++++++++++++++++++++++++++---- inst/doc/mlt.pdf |binary tests/AFT-Ex.Rout.save | 8 ++--- tests/timedep_covar.R | 4 +- tests/timedep_covar.Rout.save | 11 +++---- vignettes/mlt.Rnw | 66 ++++++++++++++++++++++++++++++++++++++---- 11 files changed, 212 insertions(+), 40 deletions(-)
Title: Basic Sensitivity Analysis of Epidemiological Results
Description: Basic sensitivity analysis of the observed relative risks adjusting
for unmeasured confounding and misclassification of the
exposure/outcome, or both. It follows the bias analysis methods and
examples from the book by Lash T.L, Fox M.P, and Fink A.K.
"Applying Quantitative Bias Analysis to Epidemiologic Data",
('Springer', 2009).
Author: Denis Haine [aut, cre] (<https://orcid.org/0000-0002-6691-7335>)
Maintainer: Denis Haine <denis.haine@gmail.com>
Diff between episensr versions 0.9.6 dated 2020-03-06 and 1.0.0 dated 2021-02-23
episensr-0.9.6/episensr/R/misclassification_cov.R |only episensr-1.0.0/episensr/DESCRIPTION | 18 episensr-1.0.0/episensr/MD5 | 129 - episensr-1.0.0/episensr/NAMESPACE | 21 episensr-1.0.0/episensr/NEWS.md | 8 episensr-1.0.0/episensr/R/boot.bias.R | 6 episensr-1.0.0/episensr/R/confounders.R | 44 episensr-1.0.0/episensr/R/confounders.emm.R | 2 episensr-1.0.0/episensr/R/confounders.evalue.R | 16 episensr-1.0.0/episensr/R/confounders.ext.R | 2 episensr-1.0.0/episensr/R/confounders.limit.R | 6 episensr-1.0.0/episensr/R/confounders.poly.R | 2 episensr-1.0.0/episensr/R/mbias.R | 66 episensr-1.0.0/episensr/R/misclassification.R | 2 episensr-1.0.0/episensr/R/misclassification.cov.R |only episensr-1.0.0/episensr/R/multidimBias.R | 49 episensr-1.0.0/episensr/R/multiple.bias.R | 29 episensr-1.0.0/episensr/R/plot.episensr.booted.R | 23 episensr-1.0.0/episensr/R/plot.episensr.probsens.R |only episensr-1.0.0/episensr/R/plot.mbias.R | 144 - episensr-1.0.0/episensr/R/print.mbias.R | 2 episensr-1.0.0/episensr/R/probsens.R | 257 +- episensr-1.0.0/episensr/R/probsens.conf.R | 214 +- episensr-1.0.0/episensr/R/probsens.irr.R | 130 + episensr-1.0.0/episensr/R/probsens.irr.conf.R | 127 - episensr-1.0.0/episensr/R/probsens.sel.R | 93 - episensr-1.0.0/episensr/R/selection.R | 3 episensr-1.0.0/episensr/R/utils.R |only episensr-1.0.0/episensr/README.md | 47 episensr-1.0.0/episensr/build/vignette.rds |binary episensr-1.0.0/episensr/inst/CITATION |only episensr-1.0.0/episensr/inst/WORDLIST |only episensr-1.0.0/episensr/inst/doc/b_probabilistic.R |only episensr-1.0.0/episensr/inst/doc/b_probabilistic.Rmd |only episensr-1.0.0/episensr/inst/doc/b_probabilistic.html |only episensr-1.0.0/episensr/inst/doc/c_multiple_bias.R |only episensr-1.0.0/episensr/inst/doc/c_multiple_bias.Rmd |only episensr-1.0.0/episensr/inst/doc/c_multiple_bias.html |only episensr-1.0.0/episensr/inst/doc/d_other_sens.R |only episensr-1.0.0/episensr/inst/doc/d_other_sens.Rmd |only episensr-1.0.0/episensr/inst/doc/d_other_sens.html |only episensr-1.0.0/episensr/inst/doc/episensr.R | 322 +-- episensr-1.0.0/episensr/inst/doc/episensr.Rmd | 606 ++---- episensr-1.0.0/episensr/inst/doc/episensr.html | 915 +++++----- episensr-1.0.0/episensr/man/confounders.Rd | 12 episensr-1.0.0/episensr/man/confounders.emm.Rd | 2 episensr-1.0.0/episensr/man/confounders.evalue.Rd | 6 episensr-1.0.0/episensr/man/confounders.ext.Rd | 2 episensr-1.0.0/episensr/man/confounders.limit.Rd | 4 episensr-1.0.0/episensr/man/confounders.poly.Rd | 2 episensr-1.0.0/episensr/man/figures |only episensr-1.0.0/episensr/man/mbias.Rd | 15 episensr-1.0.0/episensr/man/misclassification.Rd | 2 episensr-1.0.0/episensr/man/misclassification_cov.Rd | 13 episensr-1.0.0/episensr/man/multidimBias.Rd | 21 episensr-1.0.0/episensr/man/multiple.bias.Rd | 14 episensr-1.0.0/episensr/man/plot.episensr.booted.Rd | 4 episensr-1.0.0/episensr/man/plot.episensr.probsens.Rd |only episensr-1.0.0/episensr/man/plot.mbias.Rd | 27 episensr-1.0.0/episensr/man/probsens.Rd | 61 episensr-1.0.0/episensr/man/probsens.conf.Rd | 40 episensr-1.0.0/episensr/man/probsens.irr.Rd | 19 episensr-1.0.0/episensr/man/probsens.irr.conf.Rd | 34 episensr-1.0.0/episensr/man/probsens.sel.Rd | 33 episensr-1.0.0/episensr/man/selection.Rd | 3 episensr-1.0.0/episensr/tests/testthat/test-boot.R |only episensr-1.0.0/episensr/tests/testthat/test-confounders.array.R | 18 episensr-1.0.0/episensr/tests/testthat/test-confounders.ext.R |only episensr-1.0.0/episensr/tests/testthat/test-confounders.limit.R | 32 episensr-1.0.0/episensr/tests/testthat/test-misclass.R | 107 + episensr-1.0.0/episensr/tests/testthat/test-multiple.R |only episensr-1.0.0/episensr/tests/testthat/test-probsens.R | 401 +++- episensr-1.0.0/episensr/tests/testthat/test-selection.R | 18 episensr-1.0.0/episensr/vignettes/b_probabilistic.Rmd |only episensr-1.0.0/episensr/vignettes/c_multiple_bias.Rmd |only episensr-1.0.0/episensr/vignettes/d_other_sens.Rmd |only episensr-1.0.0/episensr/vignettes/episensr.Rmd | 606 ++---- 77 files changed, 2775 insertions(+), 2004 deletions(-)
Title: Explanatory Item Response Modeling for Dichotomous and
Polytomous Items
Description: Analysis of dichotomous and polytomous response data using the explanatory item response modeling framework, as described in Stanke & Bulut (2019) <doi:10.21449/ijate.515085> and De Boeck & Wilson (2004) <doi:10.1007/978-1-4757-3990-9>. Generalized linear mixed modeling is used for estimating the effects of item-related and person-related variables on dichotomous and polytomous item responses.
Author: Okan Bulut [aut, cre] (<https://orcid.org/0000-0001-5853-1267>)
Maintainer: Okan Bulut <bulut@ualberta.ca>
Diff between eirm versions 0.2.0 dated 2020-10-27 and 0.3 dated 2021-02-23
eirm-0.2.0/eirm/man/figures |only eirm-0.3/eirm/DESCRIPTION | 7 eirm-0.3/eirm/MD5 | 20 +- eirm-0.3/eirm/NAMESPACE | 52 +++-- eirm-0.3/eirm/NEWS.md |only eirm-0.3/eirm/R/eirmShiny.R |only eirm-0.3/eirm/R/plot.eirm.R | 40 ++-- eirm-0.3/eirm/R/utils-pipe.R |only eirm-0.3/eirm/build/vignette.rds |binary eirm-0.3/eirm/inst/CITATION |only eirm-0.3/eirm/inst/doc/eirm_vignette.html | 261 +++++------------------------- eirm-0.3/eirm/inst/shiny |only eirm-0.3/eirm/man/eirmShiny.Rd |only eirm-0.3/eirm/man/pipe.Rd |only 14 files changed, 118 insertions(+), 262 deletions(-)
Title: Calculate and Visualize Dominance Hierarchies
Description: Functions to calculate ADI (Average Dominance Index) and FDI (Frequency-Based Dominance Index). Functions to visualize the Data with Social Network Graphs with Dual
Directions and Music Notation Graph. 'XLConnect' or 'openxlsx' or 'RcmdrMisc' is only necessary for comfortable Excel file handling.
See ADI-FDI Hemelrijk et al. (2005) <doi:10.1163/156853905774405290> de Vries et al. (2009) <doi:10.1163/156853909X412241> Musicnotition: Chase (2006) <doi:10.1186/1742-9994-3-18>.
Author: Knut Krueger [aut, cre],
Konstanze Krueger [aut]
Maintainer: Knut Krueger <Knut.Krueger@equine-science.de>
Diff between Dominance versions 1.1.2 dated 2020-11-13 and 1.2.0 dated 2021-02-23
Dominance-1.1.2/Dominance/man/musicnotation.Rd |only Dominance-1.2.0/Dominance/DESCRIPTION | 19 +- Dominance-1.2.0/Dominance/MD5 | 32 ++-- Dominance-1.2.0/Dominance/NAMESPACE | 7 Dominance-1.2.0/Dominance/R/ADI.R | 80 +--------- Dominance-1.2.0/Dominance/R/AddDominanceDataSheet.r |only Dominance-1.2.0/Dominance/R/FDI.r | 79 +-------- Dominance-1.2.0/Dominance/R/LoadDominanceData.r |only Dominance-1.2.0/Dominance/R/Musicnotation.R | 21 +- Dominance-1.2.0/Dominance/R/Sociogram.R | 12 - Dominance-1.2.0/Dominance/R/change.action.without.response.r | 28 --- Dominance-1.2.0/Dominance/R/rename.vars.R |only Dominance-1.2.0/Dominance/build |only Dominance-1.2.0/Dominance/inst |only Dominance-1.2.0/Dominance/man/ADI.Rd | 20 +- Dominance-1.2.0/Dominance/man/AddDominanceDataSheet.Rd |only Dominance-1.2.0/Dominance/man/FDI.Rd | 15 - Dominance-1.2.0/Dominance/man/LoadDominanceData.Rd |only Dominance-1.2.0/Dominance/man/Musicnotation.Rd |only Dominance-1.2.0/Dominance/man/Sociogram.Rd | 4 Dominance-1.2.0/Dominance/man/change.action.without.response.Rd | 9 - Dominance-1.2.0/Dominance/man/rename.vars.Rd |only 22 files changed, 94 insertions(+), 232 deletions(-)
Title: Helpers for Developing Command Line Interfaces
Description: A suite of tools to build attractive command line interfaces
('CLIs'), from semantic elements: headings, lists, alerts, paragraphs,
etc. Supports custom themes via a 'CSS'-like language. It also contains a
number of lower level 'CLI' elements: rules, boxes, trees, and
'Unicode' symbols with 'ASCII' alternatives. It support ANSI colors and
text styles as well.
Author: Gábor Csárdi [aut, cre],
Hadley Wickham [ctb],
Kirill Müller [ctb],
RStudio [cph]
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Diff between cli versions 2.3.0 dated 2021-01-31 and 2.3.1 dated 2021-02-23
DESCRIPTION | 6 +++--- MD5 | 12 ++++++------ NEWS.md | 8 ++++++++ R/num-ansi-colors.R | 2 ++ R/spinner.R | 2 +- R/themes.R | 4 ++-- tests/testthat/test-headers.R | 8 ++++++++ 7 files changed, 30 insertions(+), 12 deletions(-)
Title: Importing and Working with Track and Field Data
Description: Primarily used to convert human readable track and field results into dataframes for further analysis. Results can come from central repositories like <https://www.flashresults.com/> or <http://www.deltatiming.com/>, or from individual team sites, like those for colleges. Also contains functions useful for working with track and field data.
Author: Greg Pilgrim [aut, cre] (<https://orcid.org/0000-0001-7831-442X>),
George Perry [ctb],
Caitlin Baldwin [ctb]
Maintainer: Greg Pilgrim <gpilgrim2670@gmail.com>
Diff between JumpeR versions 0.1.2 dated 2021-02-19 and 0.1.3 dated 2021-02-23
DESCRIPTION | 6 MD5 | 34 NEWS.md | 6 R/attempts_split_long.R | 7 R/attempts_split_long_helper.R | 87 R/event_parse.R | 3 R/flash_flights_parse.R | 202 +- R/flash_parse.R | 2738 ++++++++++++++--------------- R/flights_parse.R | 377 +-- R/is_link_broken.R | 1 R/read_results.R | 1 R/tf_parse.R | 9 README.md | 18 inst/extdata/flash_polevault_splits.pdf |only inst/extdata/flash_sprint.pdf |only tests/testthat.R | 8 tests/testthat/test-flash_parse_works.R | 323 ++- tests/testthat/test-relay_athletes_works.R | 26 tests/testthat/test-tf_parse_works.R | 109 - 19 files changed, 2129 insertions(+), 1826 deletions(-)
Title: Hospital Data Analysis Workflow Tools
Description: Hospital data analysis workflow tools, modeling, and automations. This library
provides many useful tools to review common administrative hospital data. Some
of these include average length of stay, readmission rates, average net pay
amounts by service lines just to name a few. The aim is to provide a simple
and consistent verb framework that takes the guesswork out of everything.
Author: Steven Sanderson [aut, cre],
Steven Sanderson [cph]
Maintainer: Steven Sanderson <spsanderson@gmail.com>
Diff between healthyR versions 0.1.1 dated 2020-12-04 and 0.1.2 dated 2021-02-23
DESCRIPTION | 9 MD5 | 22 - NAMESPACE | 4 NEWS.md | 19 R/data_tbl_functions.R | 666 +++++++++++++++++++++++++-------- R/utils.R | 139 +++--- README.md | 7 inst/doc/getting-started.html | 121 +++-- man/category_counts_tbl.Rd |only man/figures/README-gartner_chart-1.png |binary man/named_item_list.Rd |only man/save_to_excel.Rd | 66 +-- man/top_n_tbl.Rd |only man/ts_census_los_daily_tbl.Rd |only 14 files changed, 721 insertions(+), 332 deletions(-)
Title: Utilities for 'Glmnet'
Description: Provides a formula interface for the 'glmnet' package for
elasticnet regression, a method for cross-validating the alpha parameter,
and other quality-of-life tools.
Author: Microsoft [cph],
Hong Ooi [aut, cre]
Maintainer: Hong Ooi <hongooi73@gmail.com>
Diff between glmnetUtils versions 1.1.6 dated 2020-10-06 and 1.1.7 dated 2021-02-23
DESCRIPTION | 6 +++--- MD5 | 17 +++++++++-------- NEWS.md | 5 +++++ R/cvaGlmnetFormula.r | 19 +++++++++++++------ R/glmnetFormula.r | 21 ++++++++++++++++++--- R/makeModelComponents.r | 3 ++- inst/doc/intro.html | 6 +++--- man/cva.glmnet.Rd | 6 ++++-- man/glmnet.Rd | 3 +++ tests/testthat/test7_family.R |only 10 files changed, 60 insertions(+), 26 deletions(-)
Title: Causes of Outcome Learning
Description: Implementing the computational phase of the Causes of Outcome Learning approach as described in Rieckmann, Dworzynski, Arras, Lapuschkin, Samek, Arah, Rod, Ekstrom. Causes of outcome learning: A causal inference-inspired machine learning approach to disentangling common combinations of potential causes of a health outcome. medRxiv (2020) <doi:10.1101/2020.12.10.20225243>. The optional 'ggtree' package can be obtained through Bioconductor.
Author: Andreas Rieckmann [aut, cre],
Piotr Dworzynski [aut],
Leila Arras [ctb],
Claus Thorn Ekstrom [aut]
Maintainer: Andreas Rieckmann <aric@sund.ku.dk>
Diff between CoOL versions 1.0 dated 2021-02-12 and 1.0.1 dated 2021-02-23
DESCRIPTION | 8 +-- MD5 | 20 ++++----- R/CoOL_functions.R | 46 ++++++++++++++------- R/RcppExports.R | 5 +- man/CoOL_2_train_neural_network.Rd | 5 +- man/CoOL_6_dendrogram.Rd | 5 +- man/CoOL_7_prevalence_and_mean_risk_plot.Rd | 5 +- man/CoOL_8_mean_risk_contributions_by_sub_group.Rd | 5 +- man/cpp_train_network_relu.Rd | 5 +- src/RcppExports.cpp | 9 ++-- src/train_relu.cpp | 12 ++++- 11 files changed, 83 insertions(+), 42 deletions(-)
Title: Biodiversity Assessment Tools
Description: Includes algorithms to assess alpha and beta diversity
in all their dimensions (taxonomic, phylogenetic and functional).
It allows performing a number of analyses based on species
identities/abundances, phylogenetic/functional distances, trees,
convex-hulls or kernel density n-dimensional hypervolumes
depicting species relationships.
Cardoso et al. (2015) <doi:10.1111/2041-210X.12310>.
Author: Pedro Cardoso [aut, cre],
Stefano Mammola [aut],
Francois Rigal [aut],
Jose Carvalho [aut]
Maintainer: Pedro Cardoso <pedro.cardoso@helsinki.fi>
Diff between BAT versions 2.4.2 dated 2021-01-22 and 2.5.0 dated 2021-02-23
DESCRIPTION | 33 +- MD5 | 22 - NAMESPACE | 5 R/BAT.R | 564 +++++++++++++++++++++++++++++-------------- man/alpha.Rd | 2 man/beta.Rd | 2 man/coverage.Rd |only man/cwm.Rd | 3 man/dummy.Rd |only man/evenness.contribution.Rd | 2 man/hill.alpha.Rd |only man/hull.contribution.Rd | 4 man/kernel.similarity.Rd | 2 man/rao.alpha.Rd |only 14 files changed, 437 insertions(+), 202 deletions(-)
Title: Analysis Of The Interpopulation Difference In Degree of Sexual
Dimorphism Using Summary Statistics
Description: Offers a solution for the unavailability of raw data in most anthropological studies by facilitating the calculations of several sexual dimorphism related analyses using the published summary statistics of metric data (mean, standard deviation and sex specific sample size) as illustrated by the works of Greene, D. L. (1989) <doi:10.1002/ajpa.1330790113> and Konigsberg, L. W. (1991) <doi:10.1002/ajpa.1330840110>.
Author: Bassam A. Abulnoor [aut, cre] (<https://orcid.org/0000-0003-4351-2754>),
MennattAllah H. Attia [aut] (<https://orcid.org/0000-0002-2304-532X>),
Lyle W. Konigsberg [aut] (<https://orcid.org/0000-0003-4052-1575>)
Maintainer: Bassam A. Abulnoor <bassam.abulnoor@gmail.com>
Diff between TestDimorph versions 0.4.0 dated 2021-01-10 and 0.4.1 dated 2021-02-23
DESCRIPTION | 12 ++--- MD5 | 46 ++++++++++---------- NEWS.md | 6 ++ R/RawGen.R | 19 +++----- R/aovSS.R | 26 ++++------- R/aov_ss.R | 26 ++++------- R/data.R | 6 ++ R/extract_sum.R | 4 + R/helpers.R | 95 ++++++++++++++++++++---------------------- R/multivariate.R | 3 + R/raw_gen.R | 11 ++-- R/t_greene.R | 2 R/univariate.R | 3 + README.md | 2 data/Howells_summary_list.rda |only data/baboon.parms_list.rda |binary man/Howells_summary_list.Rd |only man/multi_raw.Rd | 7 --- man/multivariate.Rd | 2 man/t_greene.Rd | 2 man/t_test.Rd | 2 man/univariate.Rd | 2 man/univariate_pairwise.Rd | 2 tests/testthat/test-RawGen.R | 50 ++++++---------------- tests/testthat/test-raw_gen.R | 7 +-- 25 files changed, 156 insertions(+), 179 deletions(-)
Title: Tools to Analyse RFLP Data
Description: Provides functions to analyse DNA fragment samples (i.e. derived from RFLP-analysis) and standalone BLAST report files (i.e. DNA sequence analysis).
Author: Fabienne Flessa [aut],
Alexandra Kehl [aut] (<https://orcid.org/0000-0002-1547-0713>),
Mohammed Aslam Imtiaz [aut],
Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>
Diff between RFLPtools versions 1.6 dated 2014-08-13 and 1.8 dated 2021-02-23
RFLPtools-1.6/RFLPtools/inst/doc/RFLPtools.Rnw |only RFLPtools-1.6/RFLPtools/inst/doc/RFLPtools.pdf |only RFLPtools-1.6/RFLPtools/vignettes/HFU.jpg |only RFLPtools-1.6/RFLPtools/vignettes/RFLPtools.Rnw |only RFLPtools-1.6/RFLPtools/vignettes/logoTueb.png |only RFLPtools-1.6/RFLPtools/vignettes/logoUBT.png |only RFLPtools-1.8/RFLPtools/DESCRIPTION | 34 ++-- RFLPtools-1.8/RFLPtools/MD5 | 50 ++---- RFLPtools-1.8/RFLPtools/NAMESPACE | 6 RFLPtools-1.8/RFLPtools/NEWS | 16 + RFLPtools-1.8/RFLPtools/build/vignette.rds |binary RFLPtools-1.8/RFLPtools/data/BLASTdata.RData |binary RFLPtools-1.8/RFLPtools/data/RFLPdata.RData |binary RFLPtools-1.8/RFLPtools/data/RFLPref.RData |binary RFLPtools-1.8/RFLPtools/data/newDataGerm.RData |binary RFLPtools-1.8/RFLPtools/data/refDataGerm.RData |binary RFLPtools-1.8/RFLPtools/inst/CITATION | 21 -- RFLPtools-1.8/RFLPtools/inst/doc/RFLPtools.R | 138 ++++------------- RFLPtools-1.8/RFLPtools/inst/doc/RFLPtools.Rmd |only RFLPtools-1.8/RFLPtools/inst/doc/RFLPtools.html |only RFLPtools-1.8/RFLPtools/inst/scripts/SimulationStudy.R | 2 RFLPtools-1.8/RFLPtools/man/0RFLP-package.Rd | 19 +- RFLPtools-1.8/RFLPtools/man/RFLPdist.Rd | 4 RFLPtools-1.8/RFLPtools/man/RFLPdist2.Rd | 2 RFLPtools-1.8/RFLPtools/man/RFLPplot.Rd | 8 RFLPtools-1.8/RFLPtools/man/RFLPref.Rd | 2 RFLPtools-1.8/RFLPtools/man/RFLPrefplot.Rd | 8 RFLPtools-1.8/RFLPtools/man/sim2dist.Rd | 2 RFLPtools-1.8/RFLPtools/man/write.hclust.Rd | 4 RFLPtools-1.8/RFLPtools/vignettes/RFLPtools.Rmd |only RFLPtools-1.8/RFLPtools/vignettes/RFLPtools.bib |only 31 files changed, 142 insertions(+), 174 deletions(-)
Title: Structural Equation Modeling and Confirmatory Network Analysis
Description: Multi-group (dynamical) structural equation models in combination with confirmatory network models from cross-sectional, time-series and panel data <doi:10.31234/osf.io/8ha93>. Allows for confirmatory testing and fit as well as exploratory model search.
Author: Sacha Epskamp
Maintainer: Sacha Epskamp <mail@sachaepskamp.com>
Diff between psychonetrics versions 0.8.1 dated 2021-01-28 and 0.9 dated 2021-02-23
DESCRIPTION | 6 MD5 | 48 +-- NEWS | 13 + R/01_classes.R | 4 R/02_algebrahelpers_Solve.R | 2 R/03_modelformation_defaultoptimizer.R | 1 R/03_modelformation_matrixSetup_sigma.R | 20 + R/RcppExports.R | 12 R/a_models_dlvm1.R | 2 R/a_models_lvm.R | 2 R/a_models_meta_varcov.R | 2 R/a_models_ml_lvm.R | 2 R/a_models_tsdlvm1.R | 2 R/a_models_var1.R | 2 R/a_models_varcov.R | 2 R/c_runmodel.R | 116 +++++++-- R/f_conveneince_setoptimizer.R | 15 + build/partial.rdb |binary man/convenience.Rd | 21 + man/psychonetrics-class.Rd | 1 man/runmodel.Rd | 14 - src/02_algebrahelpers_RcppHelpers.cpp | 383 ++++++++++++++++++++++++------- src/04_generalfit_psychonetrics_BFGS.cpp | 32 ++ src/05_MLestimator_fit_Gauss_cpp.cpp | 7 src/RcppExports.cpp | 25 +- 25 files changed, 562 insertions(+), 172 deletions(-)
Title: Single Cell Analysis and Differential Expression
Description: Analyzing and interactively exploring large-scale single-cell RNA-seq datasets. 'pagoda2' primarily performs normalization and differential gene expression analysis, with an interactive application for exploring single-cell RNA-seq datasets. It performs basic tasks such as cell size normalization, gene variance normalization, and can be used to identify subpopulations and run differential expression within individual samples. 'pagoda2' was written to rapidly process modern large-scale scRNAseq datasets of approximately 1e6 cells. The companion web application allows users to explore which gene expression patterns form the different subpopulations within your data. The package also serves as the primary method for preprocessing data for conos, <https://github.com/kharchenkolab/conos>. This package interacts with data available through the 'p2data' package, which is available in a 'drat' repository. To access this data package, see the instructions at <https://github.com/kharchenkolab/pagoda2>. The size of the 'p2data' package is approximately 6 MB.
Author: Nikolas Barkas [aut],
Viktor Petukhov [aut],
Peter Kharchenko [aut],
Simon Steiger [ctb],
Evan Biederstedt [cre, aut]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between pagoda2 versions 1.0.0 dated 2021-01-28 and 1.0.1 dated 2021-02-23
DESCRIPTION | 8 MD5 | 31 - R/Pagoda2.R | 15 R/helpers.R | 57 +- README.md | 21 inst/doc/pagoda2.walkthrough.Rmd | 22 inst/doc/pagoda2.walkthrough.html | 949 ++++++++++++++------------------------ man/read10xMatrix.Rd | 2 src/RcppExports.cpp | 1 vignettes/figure_pagoda2 |only vignettes/pagoda2.walkthrough.Rmd | 22 vignettes/pagoda2.walkthrough.md |only 12 files changed, 462 insertions(+), 666 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) Tsagris, M., Papadovasilakis, Z., Lakiotaki, K. and Tsamardinos, I. (2018). Efficient feature selection on gene expression data: Which algorithm to use? BioRxiv. <doi:10.1101/431734>. e) Tsagris, M. (2019). Bayesian Network Learning with the PC Algorithm: An Improved and Correct Variation. Applied Artificial Intelligence, 33(2):101-123. <doi:10.1080/08839514.2018.1526760>. f) Tsagris, M. and Tsamardinos, I. (2019). Feature selection with the R package MXM. F1000Research 7: 1505. <doi:10.12688/f1000research.16216.2>. g) Borboudakis, G. and Tsamardinos, I. (2019). Forward-Backward Selection with Early Dropping. Journal of Machine Learning Research 20: 1-39. h) The gamma-OMP algorithm for feature selection with application to gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Accepted for publication) <doi:10.1109/TCBB.2020.3029952>.
Author: Michail Tsagris [aut, cre],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MXM versions 1.5.0 dated 2021-01-08 and 1.5.1 dated 2021-02-23
MXM-1.5.0/MXM/inst/doc/Networks_KVerrou.R |only MXM-1.5.0/MXM/inst/doc/Networks_KVerrou.Rmd |only MXM-1.5.0/MXM/inst/doc/Networks_KVerrou.html |only MXM-1.5.0/MXM/vignettes/Networks_KVerrou.Rmd |only MXM-1.5.1/MXM/DESCRIPTION | 12 +-- MXM-1.5.1/MXM/MD5 | 82 +++++++++++-------------- MXM-1.5.1/MXM/R/ci.fast.R | 2 MXM-1.5.1/MXM/R/ci.mm.R | 4 - MXM-1.5.1/MXM/R/ci.mm2.R | 3 MXM-1.5.1/MXM/R/pc.skel.R | 40 ++++++------ MXM-1.5.1/MXM/build/vignette.rds |binary MXM-1.5.1/MXM/inst/doc/FS_guide.pdf |binary MXM-1.5.1/MXM/inst/doc/MMPC_tutorial.html | 19 ++--- MXM-1.5.1/MXM/inst/doc/SES_KMVerrou_11_12.html | 48 +++++++------- MXM-1.5.1/MXM/inst/doc/article.pdf |binary MXM-1.5.1/MXM/inst/doc/guide.pdf |binary MXM-1.5.1/MXM/man/MXM-package.Rd | 24 ++----- MXM-1.5.1/MXM/man/SES.Rd | 9 +- MXM-1.5.1/MXM/man/SES.glmm.Rd | 2 MXM-1.5.1/MXM/man/SES.timeclass.Rd | 2 MXM-1.5.1/MXM/man/beta.regs.Rd | 2 MXM-1.5.1/MXM/man/bic.fsreg.Rd | 4 - MXM-1.5.1/MXM/man/bic.glm.fsreg.Rd | 4 - MXM-1.5.1/MXM/man/big.fbed.reg.Rd | 4 - MXM-1.5.1/MXM/man/big.gomp.Rd | 4 - MXM-1.5.1/MXM/man/bs.reg.Rd | 4 - MXM-1.5.1/MXM/man/cor.drop1.Rd | 4 - MXM-1.5.1/MXM/man/corfs.network.Rd | 2 MXM-1.5.1/MXM/man/cv.gomp.Rd | 2 MXM-1.5.1/MXM/man/cv.ses.Rd | 6 - MXM-1.5.1/MXM/man/fbed.gee.reg.Rd | 2 MXM-1.5.1/MXM/man/fbed.reg.Rd | 2 MXM-1.5.1/MXM/man/fbedreg.bic.Rd | 4 - MXM-1.5.1/MXM/man/glm.fsreg.Rd | 4 - MXM-1.5.1/MXM/man/glmm.bsreg.Rd | 2 MXM-1.5.1/MXM/man/group.mvbetas.Rd | 4 - MXM-1.5.1/MXM/man/lm.fsreg.Rd | 4 - MXM-1.5.1/MXM/man/mmpc2.Rd | 4 - MXM-1.5.1/MXM/man/pc.sel.Rd | 4 - MXM-1.5.1/MXM/man/pc.skel.Rd | 2 MXM-1.5.1/MXM/man/plotnetwork.Rd | 4 - MXM-1.5.1/MXM/man/sp.logiregs.Rd | 2 MXM-1.5.1/MXM/man/wald.logisticregs.Rd | 4 - MXM-1.5.1/MXM/man/zip.regs.Rd | 2 44 files changed, 159 insertions(+), 168 deletions(-)
Title: Utilities for 'Kokudo Suuchi'
Description: Provides utilities for 'Kokudo Suuchi', the GIS data service of the Japanese government.
See <https://nlftp.mlit.go.jp/index.html> for more information.
Author: Hiroaki Yutani [aut, cre] (<https://orcid.org/0000-0002-3385-7233>)
Maintainer: Hiroaki Yutani <yutani.ini@gmail.com>
Diff between kokudosuuchi versions 0.4.2 dated 2018-01-25 and 1.0.0 dated 2021-02-23
kokudosuuchi-0.4.2/kokudosuuchi/R/KSJPrefCodes.R |only kokudosuuchi-0.4.2/kokudosuuchi/R/choose_prefecture_code.R |only kokudosuuchi-0.4.2/kokudosuuchi/R/data.R |only kokudosuuchi-0.4.2/kokudosuuchi/R/getKSJSummary.R |only kokudosuuchi-0.4.2/kokudosuuchi/R/getKSJURL.R |only kokudosuuchi-0.4.2/kokudosuuchi/R/zzz.R |only kokudosuuchi-0.4.2/kokudosuuchi/data |only kokudosuuchi-0.4.2/kokudosuuchi/man/KSJMetadata_code.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/man/KSJMetadata_description_url.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/man/KSJPrefCodes.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/man/choose_prefecture_code.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/man/getKSJSummary.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/man/getKSJURL.Rd |only kokudosuuchi-0.4.2/kokudosuuchi/tests/testthat/test-API.R |only kokudosuuchi-0.4.2/kokudosuuchi/tests/testthat/test-getData.R |only kokudosuuchi-0.4.2/kokudosuuchi/tests/testthat/test-suggest_useful_links.R |only kokudosuuchi-1.0.0/kokudosuuchi/DESCRIPTION | 33 - kokudosuuchi-1.0.0/kokudosuuchi/LICENSE | 2 kokudosuuchi-1.0.0/kokudosuuchi/MD5 | 56 - kokudosuuchi-1.0.0/kokudosuuchi/NAMESPACE | 18 kokudosuuchi-1.0.0/kokudosuuchi/NEWS.md | 9 kokudosuuchi-1.0.0/kokudosuuchi/R/getKSJData.R | 131 ---- kokudosuuchi-1.0.0/kokudosuuchi/R/kokudosuuchi-package.R | 15 kokudosuuchi-1.0.0/kokudosuuchi/R/readKSJData.R |only kokudosuuchi-1.0.0/kokudosuuchi/R/rest_in_peace.R |only kokudosuuchi-1.0.0/kokudosuuchi/R/sysdata.rda |binary kokudosuuchi-1.0.0/kokudosuuchi/R/translateKSJData.R | 298 +++++++--- kokudosuuchi-1.0.0/kokudosuuchi/R/translateKSJData_individual.R |only kokudosuuchi-1.0.0/kokudosuuchi/R/util.R | 11 kokudosuuchi-1.0.0/kokudosuuchi/README.md | 286 ++++----- kokudosuuchi-1.0.0/kokudosuuchi/man/RIP_API.Rd |only kokudosuuchi-1.0.0/kokudosuuchi/man/getKSJData.Rd | 61 -- kokudosuuchi-1.0.0/kokudosuuchi/man/kokudosuuchi.Rd | 31 - kokudosuuchi-1.0.0/kokudosuuchi/man/readKSJData.Rd |only kokudosuuchi-1.0.0/kokudosuuchi/man/translateKSJData.Rd |only kokudosuuchi-1.0.0/kokudosuuchi/tests/testthat/_snaps |only kokudosuuchi-1.0.0/kokudosuuchi/tests/testthat/test-extract_KSJ_id.R |only kokudosuuchi-1.0.0/kokudosuuchi/tests/testthat/test-is_file.R | 2 kokudosuuchi-1.0.0/kokudosuuchi/tests/testthat/test-translateData.R | 101 --- 39 files changed, 479 insertions(+), 575 deletions(-)
Title: Variable Selection for Cox's Model with Interval-Censored Data
Description: Perform variable selection for Cox regression model with interval-censored data. Can deal with both low-dimensional and high-dimensional data. Case-cohort design can be incorporated. Two sets of covariates scenario can also be considered. The references are listed in the URL below.
Author: Qiwei Wu [aut, cre],
Hui Zhao [aut],
Jianguo Sun [aut]
Maintainer: Qiwei Wu <qw235@mail.missouri.edu>
Diff between CoxICPen versions 1.0.0 dated 2021-02-17 and 1.1.0 dated 2021-02-23
CoxICPen-1.0.0/CoxICPen/R/Core.R |only CoxICPen-1.1.0/CoxICPen/DESCRIPTION | 11 ++++-- CoxICPen-1.1.0/CoxICPen/MD5 | 10 +++-- CoxICPen-1.1.0/CoxICPen/NAMESPACE | 2 + CoxICPen-1.1.0/CoxICPen/R/Core_CoxICPen.R |only CoxICPen-1.1.0/CoxICPen/R/Core_CoxICPen_XZ.R |only CoxICPen-1.1.0/CoxICPen/man/CoxICPen.Rd | 46 ++++++++++++++++++--------- CoxICPen-1.1.0/CoxICPen/man/CoxICPen.XZ.Rd |only 8 files changed, 47 insertions(+), 22 deletions(-)
Title: Network Meta-Analysis using Integrated Nested Laplace
Approximations
Description: Performs network meta-analysis using integrated nested Laplace approximations ('INLA')
which is described in Guenhan, Held, and Friede (2018) <doi:10.1002/jrsm.1285>.
Includes methods to assess the heterogeneity and inconsistency in the network.
Contains more than ten different network meta-analysis dataset.
'INLA' package can be obtained from <https://www.r-inla.org>.
Author: Burak Kuersad Guenhan [aut, cre]
(<https://orcid.org/0000-0002-7454-8680>)
Maintainer: Burak Kuersad Guenhan <burak.gunhan@med.uni-goettingen.de>
Diff between nmaINLA versions 0.2.0 dated 2020-04-07 and 1.0.0 dated 2021-02-23
DESCRIPTION | 19 +++++++++------- MD5 | 52 ++++++++++++++++++++++---------------------- R/meta_inla.R | 2 - R/nma_inla.R | 7 +++-- build/vignette.rds |binary inst/doc/nmaINLA.R | 28 +++++++++++------------ inst/doc/nmaINLA.pdf |binary man/Anestheticdat.Rd | 4 ++- man/Certolizumabdat.Rd | 4 ++- man/CooperStrokedat.Rd | 6 +++-- man/Diabetesdat.Rd | 4 ++- man/Dietaryfatdat.Rd | 4 ++- man/Flourdat.Rd | 4 ++- man/IncDiabetesdat.Rd | 4 ++- man/KussHeartdat.Rd | 4 ++- man/Parkinsondat.Rd | 4 ++- man/Smokdat.Rd | 6 +++-- man/Strokedat.Rd | 4 ++- man/TBdat.Rd | 6 +++-- man/Thrombdat.Rd | 6 +++-- man/Woodsdat.Rd | 4 ++- man/create_INLA_dat.Rd | 9 +++++-- man/meta_inla.Rd | 18 +++++++++++---- man/nmaINLA.Rd | 1 man/nma_inla.Rd | 35 +++++++++++++++++++---------- man/plot_nma.Rd | 10 ++++++-- tests/testthat/test_first.R | 2 - 27 files changed, 155 insertions(+), 92 deletions(-)
Title: Core Utilities for Single-Cell RNA-Seq
Description: Core utilities for single-cell RNA-seq data analysis. Contained within are utility functions for working with differential expression (DE) matrices and count matrices, a collection of functions for manipulating and plotting data via 'ggplot2', and functions to work with cell graphs and cell embeddings. Graph-based methods include embedding kNN cell graphs into a UMAP <doi:10.21105/joss.00861>, collapsing vertices of each cluster in the graph, and propagating graph labels.
Author: Viktor Petukhov [aut],
Ramus Rydbirk [aut],
Peter Kharchenko [aut],
Evan Biederstedt [aut, cre]
Maintainer: Evan Biederstedt <evan.biederstedt@gmail.com>
Diff between sccore versions 0.1.1 dated 2020-12-14 and 0.1.2 dated 2021-02-23
DESCRIPTION | 21 ++-- MD5 | 46 +++++---- NAMESPACE | 4 R/diff_expression.R | 1 R/graph_embedding.R | 4 R/graphs.R | 165 ++++++++++++++++++++++++++++++---- R/helpers.R | 40 ++++---- R/plots.R | 203 ++++++++++++++++++++++++++++++++---------- README.md | 8 - man/collapseGraphSum.Rd | 1 man/computeChebyshevCoeffs.Rd |only man/dotPlot.Rd | 36 +++++++ man/embeddingColorsPlot.Rd | 5 - man/embeddingGroupPlot.Rd | 3 man/embeddingPlot.Rd | 27 ++--- man/getClusterGraph.Rd | 1 man/heatFilter.Rd |only man/plapply.Rd | 20 +++- man/smoothChebyshev.Rd |only man/smoothSignalOnGraph.Rd |only man/val2col.Rd |only man/val2ggcol.Rd | 2 src/Makevars |only src/Makevars.win |only src/colSumByFac.cpp | 1 src/graph_embedding.cpp | 10 +- src/include |only src/jsDist.cpp | 1 28 files changed, 454 insertions(+), 145 deletions(-)
Title: Update and Manipulate Rd Documentation Objects
Description: Functions for manipulation of R documentation objects,
including functions reprompt() and ereprompt() for updating 'Rd'
documentation for functions, methods and classes; 'Rd' macros for
citations and import of references from 'bibtex' files for use in
'Rd' files and 'roxygen2' comments; 'Rd' macros for evaluating and
inserting snippets of 'R' code and the results of its evaluation or
creating graphics on the fly; and many functions for manipulation of
references and Rd files.
Author: Georgi N. Boshnakov [aut, cre],
Duncan Murdoch [ctb]
Maintainer: Georgi N. Boshnakov <georgi.boshnakov@manchester.ac.uk>
Diff between Rdpack versions 2.1 dated 2020-11-09 and 2.1.1 dated 2021-02-23
Rdpack-2.1.1/Rdpack/DESCRIPTION | 12 - Rdpack-2.1.1/Rdpack/MD5 | 35 ++-- Rdpack-2.1.1/Rdpack/NAMESPACE | 3 Rdpack-2.1.1/Rdpack/NEWS.md | 16 + Rdpack-2.1.1/Rdpack/R/bib.R | 7 Rdpack-2.1.1/Rdpack/R/parse.R | 2 Rdpack-2.1.1/Rdpack/README.md | 81 +++++----- Rdpack-2.1.1/Rdpack/build/partial.rdb |binary Rdpack-2.1.1/Rdpack/inst/doc/Inserting_bibtex_references.pdf |binary Rdpack-2.1.1/Rdpack/inst/doc/Inserting_figures_and_evaluated_examples.pdf |binary Rdpack-2.1.1/Rdpack/man/Rdo_append_argument.Rd | 3 Rdpack-2.1.1/Rdpack/man/Rdo_reparse.Rd | 3 Rdpack-2.1.1/Rdpack/man/Rdpack-package.Rd | 8 Rdpack-2.1.1/Rdpack/man/c_Rd.Rd | 2 Rdpack-2.1.1/Rdpack/man/macros/refmacros.Rd | 1 Rdpack-2.1.1/Rdpack/man/parse_Rdpiece.Rd | 3 Rdpack-2.1.1/Rdpack/man/viewRd.Rd | 2 Rdpack-2.1.1/Rdpack/tests/testthat/test-char2Rdpiece.R | 10 - Rdpack-2.1/Rdpack/R/zzobsolete.R |only 19 files changed, 111 insertions(+), 77 deletions(-)
Title: Simulate Package Installation and Attach
Description: Simulates the process of installing a package
and then attaching it. This is a key part of the 'devtools' package as it
allows you to rapidly iterate while developing a package.
Author: Hadley Wickham [aut],
Jim Hester [aut, cre],
Winston Chang [aut],
RStudio [cph],
R Core team [ctb] (Some namespace and vignette code extracted from base
R)
Maintainer: Jim Hester <jim.hester@rstudio.com>
Diff between pkgload versions 1.1.0 dated 2020-05-29 and 1.2.0 dated 2021-02-23
pkgload-1.1.0/pkgload/src |only pkgload-1.2.0/pkgload/DESCRIPTION | 8 - pkgload-1.2.0/pkgload/MD5 | 42 +++++---- pkgload-1.2.0/pkgload/NAMESPACE | 1 pkgload-1.2.0/pkgload/NEWS.md | 35 +++++++ pkgload-1.2.0/pkgload/R/dev-help.r | 2 pkgload-1.2.0/pkgload/R/imports-env.r | 31 +----- pkgload-1.2.0/pkgload/R/load-code.r | 5 - pkgload-1.2.0/pkgload/R/load-dll.r | 35 +++++++ pkgload-1.2.0/pkgload/R/load.r | 78 +++-------------- pkgload-1.2.0/pkgload/R/namespace-env.r | 22 ++++ pkgload-1.2.0/pkgload/R/unload.r | 91 +++++++++++++------- pkgload-1.2.0/pkgload/R/utils.R | 7 - pkgload-1.2.0/pkgload/README.md | 2 pkgload-1.2.0/pkgload/man/dev_example.Rd | 2 pkgload-1.2.0/pkgload/man/help.Rd | 2 pkgload-1.2.0/pkgload/man/unload.Rd | 2 pkgload-1.2.0/pkgload/tests/testthat/test-load.r | 24 +++++ pkgload-1.2.0/pkgload/tests/testthat/testLoadLazy |only pkgload-1.2.0/pkgload/tests/testthat/testS3removed |only pkgload-1.2.0/pkgload/tests/testthat/testS3removed2 |only 21 files changed, 233 insertions(+), 156 deletions(-)
Title: Additive Partitions of Integers
Description: Additive partitions of integers. Enumerates the
partitions, unequal partitions, and restricted partitions of an
integer; the three corresponding partition functions are also
given. Set partitions and now compositions are included.
Author: Robin K. S. Hankin [aut, cre] (<https://orcid.org/0000-0001-5982-0415>),
Paul Egeler [ctb] (<https://orcid.org/0000-0001-6948-9498>)
Maintainer: Robin K. S. Hankin <hankin.robin@gmail.com>
Diff between partitions versions 1.10-1 dated 2021-02-12 and 1.10-2 dated 2021-02-23
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/partitions.R | 14 ++++++++++---- build/partitions.pdf |binary build/vignette.rds |binary inst/doc/partitionspaper.pdf |binary inst/doc/scrabble.pdf |binary inst/doc/setpartitions.pdf |binary man/conjugate.Rd | 2 ++ src/partitions.c | 7 +++---- 10 files changed, 28 insertions(+), 21 deletions(-)
Title: Interactive Statistical Data Visualization
Description: An extendable toolkit for interactive data visualization and exploration.
Author: Adrian Waddell [aut],
R. Wayne Oldford [aut, cre, ths],
Zehao Xu [ctb],
Martin Gauch [ctb]
Maintainer: R. Wayne Oldford <rwoldford@uwaterloo.ca>
Diff between loon versions 1.3.1 dated 2020-06-17 and 1.3.2 dated 2021-02-23
loon-1.3.1/loon/man/l_graph.default.Rd |only loon-1.3.1/loon/man/l_graph.graph.Rd |only loon-1.3.1/loon/man/l_graph.loongraph.Rd |only loon-1.3.1/loon/man/l_plot.decomposed.ts.Rd |only loon-1.3.1/loon/man/l_plot.default.Rd |only loon-1.3.1/loon/man/l_plot.density.Rd |only loon-1.3.1/loon/man/l_plot.map.Rd |only loon-1.3.1/loon/man/l_plot.stl.Rd |only loon-1.3.1/loon/man/l_plot3D.default.Rd |only loon-1.3.1/loon/tests/testthat/testthat.R |only loon-1.3.2/loon/DESCRIPTION | 17 loon-1.3.2/loon/MD5 | 263 +-- loon-1.3.2/loon/NAMESPACE | 22 loon-1.3.2/loon/NEWS.md | 58 loon-1.3.2/loon/R/L2_Distance.R | 2 loon-1.3.2/loon/R/aes_settings.R |only loon-1.3.2/loon/R/datasets.R | 2 loon-1.3.2/loon/R/defaultLinkableStates.R |only loon-1.3.2/loon/R/facet_layout.R | 128 + loon-1.3.2/loon/R/get_facets.R | 452 +++--- loon-1.3.2/loon/R/graphutils.R | 300 ++-- loon-1.3.2/loon/R/inspectors.R | 21 loon-1.3.2/loon/R/l_bind.R | 204 +- loon-1.3.2/loon/R/l_compound.R | 2 loon-1.3.2/loon/R/l_configure.R | 2 loon-1.3.2/loon/R/l_facet.R | 58 loon-1.3.2/loon/R/l_getFromPath.R | 73 loon-1.3.2/loon/R/l_getScaledData.R |only loon-1.3.2/loon/R/l_glyphs.R | 7 loon-1.3.2/loon/R/l_graph.R | 168 +- loon-1.3.2/loon/R/l_help.R | 4 loon-1.3.2/loon/R/l_hist.R | 750 +++------- loon-1.3.2/loon/R/l_layer_contourLines.R | 2 loon-1.3.2/loon/R/l_layer_map.R | 33 loon-1.3.2/loon/R/l_layer_smooth.R |only loon-1.3.2/loon/R/l_linkingWarning.R |only loon-1.3.2/loon/R/l_loonWidgets.R | 242 +-- loon-1.3.2/loon/R/l_modifiedLinkedStates.R |only loon-1.3.2/loon/R/l_ng_ranges.R | 2 loon-1.3.2/loon/R/l_pairs.R | 596 +++++-- loon-1.3.2/loon/R/l_plot.R | 498 ++---- loon-1.3.2/loon/R/l_plot3D.R | 624 +++----- loon-1.3.2/loon/R/l_plot_decomposed_ts.R | 65 loon-1.3.2/loon/R/l_plot_density.R | 39 loon-1.3.2/loon/R/l_plot_map.R |only loon-1.3.2/loon/R/l_plot_stl.R | 66 loon-1.3.2/loon/R/l_plot_ts.R | 222 ++ loon-1.3.2/loon/R/l_predict.R |only loon-1.3.2/loon/R/l_serialaxes.R | 261 +-- loon-1.3.2/loon/R/l_toplevel.R | 64 loon-1.3.2/loon/R/l_web.R | 8 loon-1.3.2/loon/R/loon-package.R | 2 loon-1.3.2/loon/R/loonFacets.R | 476 ++++-- loon-1.3.2/loon/R/loonGrob.R | 122 - loon-1.3.2/loon/R/loonGrob_l_layer_graph.R | 4 loon-1.3.2/loon/R/loonGrob_l_layer_scatterplot.R | 88 - loon-1.3.2/loon/R/loonGrob_l_pairs.R | 3 loon-1.3.2/loon/R/loonGrob_l_serialaxes.R | 232 +-- loon-1.3.2/loon/R/loonobject.R | 2 loon-1.3.2/loon/README.md | 75 - loon-1.3.2/loon/build/vignette.rds |binary loon-1.3.2/loon/demo/periodic_table.R | 49 loon-1.3.2/loon/inst/doc/introduction.html | 416 ++--- loon-1.3.2/loon/inst/doc/savingLoonPlots.html | 194 +- loon-1.3.2/loon/inst/doc/teaching-example-smoothing.R | 31 loon-1.3.2/loon/inst/doc/teaching-example-smoothing.Rmd | 37 loon-1.3.2/loon/inst/doc/teaching-example-smoothing.html | 369 ++-- loon-1.3.2/loon/inst/tcl/loon/library/listfns.tcl | 110 + loon-1.3.2/loon/inst/tcl/loon/library/oo_Histogram_View.tcl | 26 loon-1.3.2/loon/inst/tcl/loon/library/oo_LayerVisual.tcl | 35 loon-1.3.2/loon/inst/tcl/loon/library/oo_LayersInspector.tcl | 134 - loon-1.3.2/loon/inst/tcl/loon/library/oo_LineVisual.tcl | 28 loon-1.3.2/loon/inst/tcl/loon/library/oo_ParallelCoordinatesVisual.tcl | 214 +- loon-1.3.2/loon/inst/tcl/loon/library/oo_Plot_Model.tcl | 36 loon-1.3.2/loon/inst/tcl/loon/library/oo_Plot_View.tcl | 118 - loon-1.3.2/loon/inst/tcl/loon/library/oo_PolygonGlyph.tcl | 34 loon-1.3.2/loon/inst/tcl/loon/library/oo_PolygonGlyphVisual.tcl | 49 loon-1.3.2/loon/inst/tcl/loon/library/oo_PrimitiveLayer.tcl | 12 loon-1.3.2/loon/inst/tcl/loon/library/oo_Serialaxes.tcl | 109 - loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesAbstractVisual.tcl | 98 - loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesGlyphInspector.tcl | 38 loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesGlyphVisual.tcl | 347 +++- loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesInspector.tcl |only loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesInspectorAnalysis.tcl | 121 - loon-1.3.2/loon/inst/tcl/loon/library/oo_SerialaxesLayer.tcl |only loon-1.3.2/loon/inst/tcl/loon/library/oo_Serialaxes_Model.tcl | 71 loon-1.3.2/loon/inst/tcl/loon/library/oo_Serialaxes_View.tcl | 134 + loon-1.3.2/loon/inst/tcl/loon/library/oo_Serialaxes_Widget.tcl | 20 loon-1.3.2/loon/inst/tcl/loon/library/oo_StarglyphsStackedVisual.tcl | 282 ++- loon-1.3.2/loon/inst/tcl/loon/library/oo_withLayers.tcl | 293 +-- loon-1.3.2/loon/inst/tcl/loon/library/x_widgets.tcl | 58 loon-1.3.2/loon/inst/tcl/loon/pkgIndex.tcl | 2 loon-1.3.2/loon/man/UsAndThem.Rd | 2 loon-1.3.2/loon/man/as.graph.Rd | 14 loon-1.3.2/loon/man/as.loongraph.Rd | 4 loon-1.3.2/loon/man/completegraph.Rd | 8 loon-1.3.2/loon/man/facet_grid_layout.Rd | 10 loon-1.3.2/loon/man/facet_wrap_layout.Rd | 6 loon-1.3.2/loon/man/figures/brushing.gif |only loon-1.3.2/loon/man/figures/facetting.PNG |only loon-1.3.2/loon/man/figures/histDemo.gif |only loon-1.3.2/loon/man/figures/plot3D.gif |only loon-1.3.2/loon/man/figures/zooming_panning.gif |only loon-1.3.2/loon/man/l_bind_canvas.Rd | 4 loon-1.3.2/loon/man/l_bind_item.Rd | 2 loon-1.3.2/loon/man/l_bind_item_reorder.Rd | 2 loon-1.3.2/loon/man/l_facet.Rd | 27 loon-1.3.2/loon/man/l_getFromPath.Rd | 5 loon-1.3.2/loon/man/l_getScaledData.Rd |only loon-1.3.2/loon/man/l_glyph_add_serialaxes.Rd | 5 loon-1.3.2/loon/man/l_graph.Rd | 34 loon-1.3.2/loon/man/l_help.Rd | 2 loon-1.3.2/loon/man/l_hist.Rd | 108 + loon-1.3.2/loon/man/l_info_states.Rd | 3 loon-1.3.2/loon/man/l_layer.map.Rd | 5 loon-1.3.2/loon/man/l_layer_contourLines.Rd | 7 loon-1.3.2/loon/man/l_layer_heatImage.Rd | 5 loon-1.3.2/loon/man/l_layer_rasterImage.Rd | 5 loon-1.3.2/loon/man/l_layer_smooth.Rd |only loon-1.3.2/loon/man/l_loonWidgets.Rd | 6 loon-1.3.2/loon/man/l_loon_inspector.Rd | 7 loon-1.3.2/loon/man/l_ng_ranges.scagnostics.Rd | 2 loon-1.3.2/loon/man/l_pairs.Rd | 17 loon-1.3.2/loon/man/l_plot.Rd | 360 ++++ loon-1.3.2/loon/man/l_plot3D.Rd | 183 ++ loon-1.3.2/loon/man/l_plot_ts.Rd | 15 loon-1.3.2/loon/man/l_predict.Rd |only loon-1.3.2/loon/man/l_scale3D.Rd | 1 loon-1.3.2/loon/man/l_serialaxes.Rd | 80 - loon-1.3.2/loon/man/l_serialaxes_inspector.Rd | 2 loon-1.3.2/loon/man/l_state_names.Rd | 3 loon-1.3.2/loon/man/l_toplevel.Rd |only loon-1.3.2/loon/man/l_web.Rd | 4 loon-1.3.2/loon/man/linegraph.Rd | 6 loon-1.3.2/loon/man/linegraph.loongraph.Rd | 2 loon-1.3.2/loon/man/loon.Rd | 4 loon-1.3.2/loon/man/loonGrob.Rd | 1 loon-1.3.2/loon/man/loongraph.Rd | 6 loon-1.3.2/loon/man/names.loon.Rd | 3 loon-1.3.2/loon/man/plot.loongraph.Rd | 2 loon-1.3.2/loon/tests/testthat.R |only loon-1.3.2/loon/tests/testthat/test_andrews.R |only loon-1.3.2/loon/tests/testthat/test_facets.R | 172 +- loon-1.3.2/loon/tests/testthat/test_l_compound_withParents.R |only loon-1.3.2/loon/tests/testthat/test_linking.R | 106 - loon-1.3.2/loon/tests/testthat/test_smooth.R |only loon-1.3.2/loon/tests/testthat/test_sync.R |only loon-1.3.2/loon/tests/testthat/test_widgetPaths.R | 30 loon-1.3.2/loon/tests/testthat/test_zeroOneDimData.R |only loon-1.3.2/loon/vignettes/teaching-example-smoothing.Rmd | 37 150 files changed, 6436 insertions(+), 4595 deletions(-)
Title: Image Processing Library Based on 'CImg'
Description: Fast image processing for images in up to 4 dimensions (two spatial
dimensions, one time/depth dimension, one colour dimension). Provides most
traditional image processing tools (filtering, morphology, transformations,
etc.) as well as various functions for easily analysing image data using R. The
package wraps 'CImg', <http://cimg.eu>, a simple, modern C++ library for image
processing.
Author: Simon Barthelme [aut],
David Tschumperle [ctb],
Jan Wijffels [ctb],
Haz Edine Assemlal [ctb],
Shota Ochi [cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between imager versions 0.42.3 dated 2020-05-11 and 0.42.7 dated 2021-02-23
DESCRIPTION | 14 MD5 | 46 - R/RcppExports.R | 2 R/cimg_class.R | 4 R/interactive.R | 2 R/utils.R | 2 build/vignette.rds |binary configure | 1179 ++++++++++++++----------------------------- configure.ac | 101 ++- inst/doc/gettingstarted.Rmd | 6 inst/doc/gettingstarted.html | 8 inst/doc/pixsets.Rmd | 2 inst/doc/pixsets.html | 2 man/display.Rd | 2 man/display.cimg.Rd | 2 man/grab.Rd | 3 man/interact.Rd | 1 man/play.Rd | 2 man/resize_uniform.Rd | 2 src/Makevars.in | 2 src/display.cpp | 36 + src/interact.cpp | 13 vignettes/gettingstarted.Rmd | 6 vignettes/pixsets.Rmd | 2 24 files changed, 572 insertions(+), 867 deletions(-)
Title: Perform and Display Google Trends Queries
Description: An interface for retrieving and displaying the information
returned online by Google Trends is provided. Trends (number of
hits) over the time as well as geographic representation of the
results can be displayed.
Author: Philippe Massicotte [aut, cre],
Dirk Eddelbuettel [aut]
Maintainer: Philippe Massicotte <pmassicotte@hotmail.com>
Diff between gtrendsR versions 1.4.7 dated 2020-09-12 and 1.4.8 dated 2021-02-23
DESCRIPTION | 6 +- MD5 | 24 +++++------ NEWS.md | 10 ++++ R/related_topics.R | 56 +++++++++++++++++++++----- R/setHandleParameters.R | 15 ++++++ R/zzz.R | 15 ++++++ README.md | 8 +++ inst/tinytest/test_encoding_does_not_change.R | 13 +++++- inst/tinytest/test_gprop.R | 12 +++++ inst/tinytest/test_not_empty_results.R | 15 +++++- inst/tinytest/test_timespans.R | 10 ++++ man/setHandleParameters.Rd | 13 +++++- tests/tinytest.R | 3 - 13 files changed, 162 insertions(+), 38 deletions(-)
Title: Significance Brackets for 'ggplot2'
Description: Enrich your 'ggplots' with group-wise comparisons.
This package provides an easy way to indicate if two groups are
significantly different. Commonly this is shown by a bracket on top
connecting the groups of interest which itself is annotated with the
level of significance (NS, *, **, ***). The package provides a single
layer (geom_signif()) that takes the groups for comparison and the
test (t.test(), wilcox.text() etc.) as arguments and adds the
annotation to the plot.
Author: Constantin Ahlmann-Eltze [aut, cre, ctb]
(<https://orcid.org/0000-0002-3762-068X>, @const_ae),
Indrajeet Patil [aut, ctb] (<https://orcid.org/0000-0003-1995-6531>,
@patilindrajeets)
Maintainer: Constantin Ahlmann-Eltze <artjom31415@googlemail.com>
Diff between ggsignif versions 0.6.0 dated 2019-08-08 and 0.6.1 dated 2021-02-23
ggsignif-0.6.0/ggsignif/R/experiments.R |only ggsignif-0.6.0/ggsignif/R/significance_annotation.R |only ggsignif-0.6.0/ggsignif/R/util.R |only ggsignif-0.6.0/ggsignif/tests/example.png |only ggsignif-0.6.0/ggsignif/tests/testthat/test-new.R |only ggsignif-0.6.0/ggsignif/tests/testthat/test-significance_annotation.R |only ggsignif-0.6.0/ggsignif/tools |only ggsignif-0.6.1/ggsignif/DESCRIPTION | 52 ggsignif-0.6.1/ggsignif/MD5 | 51 ggsignif-0.6.1/ggsignif/NEWS.md | 43 ggsignif-0.6.1/ggsignif/R/geom_signif.R |only ggsignif-0.6.1/ggsignif/R/utilities.R |only ggsignif-0.6.1/ggsignif/README.md | 120 +- ggsignif-0.6.1/ggsignif/build/vignette.rds |binary ggsignif-0.6.1/ggsignif/inst/WORDLIST |only ggsignif-0.6.1/ggsignif/inst/doc/intro.R | 37 ggsignif-0.6.1/ggsignif/inst/doc/intro.Rmd | 49 ggsignif-0.6.1/ggsignif/inst/doc/intro.html | 532 ++++------ ggsignif-0.6.1/ggsignif/man/figures |only ggsignif-0.6.1/ggsignif/man/stat_signif.Rd | 163 ++- ggsignif-0.6.1/ggsignif/tests/figs |only ggsignif-0.6.1/ggsignif/tests/spelling.R |only ggsignif-0.6.1/ggsignif/tests/testthat/Rplots.pdf |binary ggsignif-0.6.1/ggsignif/tests/testthat/_snaps |only ggsignif-0.6.1/ggsignif/tests/testthat/test-errors.R |only ggsignif-0.6.1/ggsignif/tests/testthat/test-geom_signific_basic.R |only ggsignif-0.6.1/ggsignif/tests/testthat/test-geom_signific_strict.R |only ggsignif-0.6.1/ggsignif/tests/testthat/test-parsing.R |only ggsignif-0.6.1/ggsignif/tests/testthat/test-snapshot_data.R |only ggsignif-0.6.1/ggsignif/tests/testthat/test-vdiffr.R |only ggsignif-0.6.1/ggsignif/vignettes/intro.Rmd | 49 31 files changed, 577 insertions(+), 519 deletions(-)
Title: An Implementation of Grammar of Graphics for Graphs and Networks
Description: The grammar of graphics as implemented in ggplot2 is a poor fit for
graph and network visualizations due to its reliance on tabular data input.
ggraph is an extension of the ggplot2 API tailored to graph visualizations
and provides the same flexible approach to building up plots layer by layer.
Author: Thomas Lin Pedersen [cre, aut]
(<https://orcid.org/0000-0002-5147-4711>),
RStudio [cph]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>
Diff between ggraph versions 2.0.4 dated 2020-11-16 and 2.0.5 dated 2021-02-23
DESCRIPTION | 6 MD5 | 33 +-- NEWS.md | 5 R/geom_conn_bundle.R | 2 R/layout_fabric.R | 2 R/layout_matrix.R | 2 R/layout_treemap.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/doc/Edges.html | 365 ++++++++++++++++------------------------ inst/doc/Layouts.html | 113 ++---------- inst/doc/Nodes.html | 83 +-------- inst/doc/tidygraph.html | 77 -------- man/geom_conn_bundle.Rd | 2 man/layout_tbl_graph_fabric.Rd | 2 man/layout_tbl_graph_matrix.Rd | 2 man/layout_tbl_graph_treemap.Rd | 2 src/Makevars |only src/Makevars.win |only 19 files changed, 231 insertions(+), 467 deletions(-)
Title: Robust Analytical Methods for Evaluating Educational
Interventions using Randomised Controlled Trials Designs
Description: Analysing data from evaluations of educational interventions using a randomised controlled trial design. Various analytical tools to perform sensitivity analysis using different methods are supported (e.g. frequentist models with bootstrapping and permutations options, Bayesian models). The included commands can be used for simple randomised trials, cluster randomised trials and multisite trials. The methods can also be used more widely beyond education trials. This package can be used to evaluate other intervention designs using Frequentist and Bayesian multilevel models.
Author: Germaine Uwimpuhwe, Akansha Singh, Steve Higgins, ZhiMin Xiao, Ewoud De Troyer and Adetayo Kasim
Maintainer: Germaine Uwimpuhwe <germaine.uwimpuhwe@durham.ac.uk>
Diff between eefAnalytics versions 1.0.8 dated 2020-10-22 and 1.0.10 dated 2021-02-23
eefAnalytics-1.0.10/eefAnalytics/DESCRIPTION | 18 eefAnalytics-1.0.10/eefAnalytics/MD5 | 51 eefAnalytics-1.0.10/eefAnalytics/NAMESPACE | 19 eefAnalytics-1.0.10/eefAnalytics/R/Print_Summary.R |only eefAnalytics-1.0.10/eefAnalytics/R/crtBayes.R |only eefAnalytics-1.0.10/eefAnalytics/R/crtFreq.R |only eefAnalytics-1.0.10/eefAnalytics/R/globals.R | 2 eefAnalytics-1.0.10/eefAnalytics/R/mstBayes.R |only eefAnalytics-1.0.10/eefAnalytics/R/mstFreq.R |only eefAnalytics-1.0.10/eefAnalytics/R/plotfunctions.R | 292 +-- eefAnalytics-1.0.10/eefAnalytics/R/srtBayes.R |only eefAnalytics-1.0.10/eefAnalytics/R/srtFreq.R |only eefAnalytics-1.0.10/eefAnalytics/build/vignette.rds |binary eefAnalytics-1.0.10/eefAnalytics/inst/doc/eefAnalytics.Rmd | 577 ++++--- eefAnalytics-1.0.10/eefAnalytics/inst/doc/eefAnalytics.html | 782 +++++----- eefAnalytics-1.0.10/eefAnalytics/inst/examples/SummaryExample.R |only eefAnalytics-1.0.10/eefAnalytics/inst/examples/printExample.R |only eefAnalytics-1.0.10/eefAnalytics/man/ComparePlot.Rd | 10 eefAnalytics-1.0.10/eefAnalytics/man/crtBayes.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/crtData.Rd | 6 eefAnalytics-1.0.10/eefAnalytics/man/crtFREQ.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/mstBayes.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/mstData.Rd | 6 eefAnalytics-1.0.10/eefAnalytics/man/mstFREQ.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/plot.eefAnalytics.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/print.Rd |only eefAnalytics-1.0.10/eefAnalytics/man/srtBayes.Rd | 20 eefAnalytics-1.0.10/eefAnalytics/man/srtFREQ.Rd | 12 eefAnalytics-1.0.10/eefAnalytics/man/summary.Rd |only eefAnalytics-1.0.10/eefAnalytics/vignettes/EEFanalytics.pdf |binary eefAnalytics-1.0.10/eefAnalytics/vignettes/eefAnalytics.Rmd | 577 ++++--- eefAnalytics-1.0.8/eefAnalytics/NEWS.md |only eefAnalytics-1.0.8/eefAnalytics/R/eefAnalytics_14_09_2020.R |only 33 files changed, 1416 insertions(+), 1016 deletions(-)
Title: A Multi-Modal Simulator for Spearheading Single-Cell Omics
Analyses
Description: A novel, multi-modal simulation engine for
studying dynamic cellular processes at single-cell resolution. 'dyngen'
is more flexible than current single-cell simulation engines. It
allows better method development and benchmarking, thereby stimulating
development and testing of novel computational methods. Cannoodt et
al. (2020) <doi:10.1101/2020.02.06.936971>.
Author: Robrecht Cannoodt [aut, cre, cph]
(<https://orcid.org/0000-0003-3641-729X>),
Wouter Saelens [aut] (<https://orcid.org/0000-0002-7114-6248>)
Maintainer: Robrecht Cannoodt <rcannood@gmail.com>
Diff between dyngen versions 0.4.0 dated 2020-09-10 and 1.0.0 dated 2021-02-23
dyngen-0.4.0/dyngen/R/2_backbone.R |only dyngen-0.4.0/dyngen/R/2a_modnet_pieces.R |only dyngen-0.4.0/dyngen/R/2b_backbone_lego.R |only dyngen-0.4.0/dyngen/R/2c_backbones.R |only dyngen-0.4.0/dyngen/R/3_tf_network.R |only dyngen-0.4.0/dyngen/R/4_feature_network.R |only dyngen-0.4.0/dyngen/R/5_kinetics.R |only dyngen-0.4.0/dyngen/R/6_gold_standard.R |only dyngen-0.4.0/dyngen/R/7_simulation.R |only dyngen-0.4.0/dyngen/R/8_experiment.R |only dyngen-0.4.0/dyngen/R/9_dynwrap.R |only dyngen-0.4.0/dyngen/inst/doc/showcase_backbones.html |only dyngen-0.4.0/dyngen/inst/doc/showcase_backbones.html.asis |only dyngen-0.4.0/dyngen/man/figures/README_bblego-1.png |only dyngen-0.4.0/dyngen/man/figures/README_bifurcatingloop_plot-1.png |only dyngen-0.4.0/dyngen/man/figures/README_compare-1.png |only dyngen-0.4.0/dyngen/man/figures/README_dyno-1.png |only dyngen-0.4.0/dyngen/man/figures/README_dynplot-1.png |only dyngen-0.4.0/dyngen/man/figures/README_dynplot-2.png |only dyngen-0.4.0/dyngen/man/figures/README_expression_sim-1.png |only dyngen-0.4.0/dyngen/man/figures/README_gold_pt-1.png |only dyngen-0.4.0/dyngen/man/figures/README_gold_pt-2.png |only dyngen-0.4.0/dyngen/man/figures/README_gold_standard-1.png |only dyngen-0.4.0/dyngen/man/figures/README_init-1.png |only dyngen-0.4.0/dyngen/man/figures/README_init-2.png |only dyngen-0.4.0/dyngen/man/figures/README_oneshot_plot-1.png |only dyngen-0.4.0/dyngen/man/figures/README_oneshot_plot-2.png |only dyngen-0.4.0/dyngen/man/figures/README_oneshot_plot-3.png |only dyngen-0.4.0/dyngen/man/figures/README_oneshot_run-1.png |only dyngen-0.4.0/dyngen/man/figures/README_overlay-1.png |only dyngen-0.4.0/dyngen/man/figures/README_simulations-1.png |only dyngen-0.4.0/dyngen/man/figures/README_ssa-1.png |only dyngen-0.4.0/dyngen/man/figures/README_ssa-2.png |only dyngen-0.4.0/dyngen/man/figures/README_target_network-1.png |only dyngen-0.4.0/dyngen/man/figures/README_target_network-2.png |only dyngen-0.4.0/dyngen/man/figures/README_tf_network-1.png |only dyngen-0.4.0/dyngen/man/figures/generation_overview_v1.png |only dyngen-0.4.0/dyngen/man/figures/generation_overview_v1.svg |only dyngen-0.4.0/dyngen/man/wrap_dataset.Rd |only dyngen-0.4.0/dyngen/vignettes/showcase_backbones.html.asis |only dyngen-1.0.0/dyngen/DESCRIPTION | 18 dyngen-1.0.0/dyngen/LICENSE | 4 dyngen-1.0.0/dyngen/MD5 | 138 - dyngen-1.0.0/dyngen/NAMESPACE | 21 dyngen-1.0.0/dyngen/NEWS.md | 68 dyngen-1.0.0/dyngen/R/0a_backbone.R |only dyngen-1.0.0/dyngen/R/0b_modnet_pieces.R |only dyngen-1.0.0/dyngen/R/0c_backbone_lego.R |only dyngen-1.0.0/dyngen/R/0d_backbones.R |only dyngen-1.0.0/dyngen/R/1_initialisation.R | 55 dyngen-1.0.0/dyngen/R/2_tf_network.R |only dyngen-1.0.0/dyngen/R/3_feature_network.R |only dyngen-1.0.0/dyngen/R/4_kinetics.R |only dyngen-1.0.0/dyngen/R/5_gold_standard.R |only dyngen-1.0.0/dyngen/R/6_simulation.R |only dyngen-1.0.0/dyngen/R/7_experiment.R |only dyngen-1.0.0/dyngen/R/8_convert.R |only dyngen-1.0.0/dyngen/R/combine_models.R |only dyngen-1.0.0/dyngen/R/generate_dataset.R | 92 dyngen-1.0.0/dyngen/R/package.R | 136 + dyngen-1.0.0/dyngen/R/plotting.R | 154 + dyngen-1.0.0/dyngen/R/timings.R |only dyngen-1.0.0/dyngen/README.md | 180 - dyngen-1.0.0/dyngen/build/vignette.rds |binary dyngen-1.0.0/dyngen/data/example_model.rda |binary dyngen-1.0.0/dyngen/data/realcounts.rda |binary dyngen-1.0.0/dyngen/inst/CITATION | 1 dyngen-1.0.0/dyngen/inst/doc/getting_started.html | 933 +--------- dyngen-1.0.0/dyngen/inst/doc/installation.html |only dyngen-1.0.0/dyngen/inst/doc/installation.html.asis |only dyngen-1.0.0/dyngen/man/backbone.Rd | 21 dyngen-1.0.0/dyngen/man/backbone_models.Rd | 8 dyngen-1.0.0/dyngen/man/bblego.Rd | 2 dyngen-1.0.0/dyngen/man/combine_models.Rd |only dyngen-1.0.0/dyngen/man/convert.Rd |only dyngen-1.0.0/dyngen/man/dyngen.Rd | 173 + dyngen-1.0.0/dyngen/man/figures/overview.png |only dyngen-1.0.0/dyngen/man/generate_cells.Rd | 19 dyngen-1.0.0/dyngen/man/generate_dataset.Rd | 36 dyngen-1.0.0/dyngen/man/generate_experiment.Rd | 28 dyngen-1.0.0/dyngen/man/generate_feature_network.Rd | 19 dyngen-1.0.0/dyngen/man/generate_gold_standard.Rd | 28 dyngen-1.0.0/dyngen/man/generate_kinetics.Rd | 21 dyngen-1.0.0/dyngen/man/generate_tf_network.Rd | 25 dyngen-1.0.0/dyngen/man/get_timings.Rd |only dyngen-1.0.0/dyngen/man/initialise_model.Rd | 25 dyngen-1.0.0/dyngen/man/kinetics_noise.Rd | 2 dyngen-1.0.0/dyngen/man/plot_backbone_modulenet.Rd | 2 dyngen-1.0.0/dyngen/man/plot_backbone_statenet.Rd | 2 dyngen-1.0.0/dyngen/man/plot_experiment_dimred.Rd |only dyngen-1.0.0/dyngen/man/plot_feature_network.Rd | 2 dyngen-1.0.0/dyngen/man/plot_gold_mappings.Rd | 4 dyngen-1.0.0/dyngen/man/plot_gold_simulations.Rd | 2 dyngen-1.0.0/dyngen/man/plot_simulation_expression.Rd | 2 dyngen-1.0.0/dyngen/man/plot_simulations.Rd | 4 dyngen-1.0.0/dyngen/man/realcounts.Rd | 2 dyngen-1.0.0/dyngen/tests/testthat/test-1_initialisation.R | 6 dyngen-1.0.0/dyngen/tests/testthat/test-combine_models.R |only dyngen-1.0.0/dyngen/tests/testthat/test-generate_dataset.R | 77 dyngen-1.0.0/dyngen/tests/testthat/test-generate_partitions.R | 8 dyngen-1.0.0/dyngen/vignettes/installation.html.asis |only 101 files changed, 1032 insertions(+), 1286 deletions(-)
Title: Modules to Import and Manipulate Data in 'Shiny'
Description: 'Shiny' modules to import data into an application or 'addin'
from various sources, and to manipulate them after that.
Author: Victor Perrier [aut, cre, cph],
Fanny Meyer [aut],
Zauad Shahreer Abeer [aut]
Maintainer: Victor Perrier <victor.perrier@dreamrs.fr>
Diff between datamods versions 1.0.1 dated 2021-02-16 and 1.1.0 dated 2021-02-23
DESCRIPTION | 14 MD5 | 51 - NAMESPACE | 1 NEWS.md | 7 R/filter-data.R | 7 R/i18n.R |only R/import-copypaste.R | 301 +++--- R/import-file.R | 517 +++++------ R/import-globalenv.R | 617 +++++++------- R/import-googlesheets.R | 399 ++++----- R/import-modal.R | 783 +++++++++--------- R/show_data.R | 103 +- R/update-variables.R | 1299 ++++++++++++++---------------- R/utils-shiny.R | 346 ++++--- R/validation.R | 610 +++++++------- R/zzz.R | 2 README.md | 7 build/vignette.rds |binary inst/doc/datamods.Rmd | 2 inst/doc/datamods.html | 2 inst/doc/i18n.R |only inst/doc/i18n.Rmd |only inst/doc/i18n.html |only inst/i18n |only man/filter-data.Rd | 9 man/show_data.Rd | 37 tests/testthat/test-i18n.R |only tests/testthat/test-import-googlesheets.R | 34 vignettes/datamods.Rmd | 2 vignettes/i18n.Rmd |only 30 files changed, 2625 insertions(+), 2525 deletions(-)
Title: Tools to Create, Modify and Manage 'CWB' Corpora
Description: The 'Corpus Workbench' ('CWB', <http://cwb.sourceforge.net/>) offers a classic and mature
approach for working with large, linguistically and structurally annotated corpora. The 'CWB'
is memory efficient and its design makes running queries fast (Evert and Hardie 2011,
<http://www.stefan-evert.de/PUB/EvertHardie2011.pdf>). The 'cwbtools' package offers
pure R tools to create indexed corpus files as well as high-level wrappers for the original C
implementation of CWB as exposed by the 'RcppCWB' package
<https://CRAN.R-project.org/package=RcppCWB>. Additional functionality to add and
modify annotations of corpora from within R makes working with CWB indexed corpora
much more flexible and convenient. The 'cwbtools' package in combination with the R packages
'RcppCWB' (<https://CRAN.R-project.org/package=RcppCWB>) and 'polmineR'
(<https://CRAN.R-project.org/package=polmineR>) offers a lightweight infrastructure
to support the combination of quantitative and qualitative approaches for working
with textual data.
Author: Andreas Blaette [aut, cre],
Christoph Leonhardt [ctb]
Maintainer: Andreas Blaette <andreas.blaette@uni-due.de>
Diff between cwbtools versions 0.3.2 dated 2021-02-17 and 0.3.3 dated 2021-02-23
cwbtools-0.3.2/cwbtools/inst/doc/europarl.R |only cwbtools-0.3.2/cwbtools/inst/doc/europarl.Rmd |only cwbtools-0.3.2/cwbtools/inst/doc/europarl.html |only cwbtools-0.3.2/cwbtools/vignettes/europarl.Rmd |only cwbtools-0.3.3/cwbtools/DESCRIPTION | 12 - cwbtools-0.3.3/cwbtools/MD5 | 44 +--- cwbtools-0.3.3/cwbtools/NEWS.md | 23 ++ cwbtools-0.3.3/cwbtools/R/corpus.R | 42 +++ cwbtools-0.3.3/cwbtools/R/directories.R | 13 - cwbtools-0.3.3/cwbtools/R/pkg.R | 1 cwbtools-0.3.3/cwbtools/build/vignette.rds |binary cwbtools-0.3.3/cwbtools/inst/doc/opennlp.R | 74 +++--- cwbtools-0.3.3/cwbtools/inst/doc/opennlp.Rmd | 10 cwbtools-0.3.3/cwbtools/inst/doc/opennlp.html | 4 cwbtools-0.3.3/cwbtools/inst/doc/sentences.R | 12 - cwbtools-0.3.3/cwbtools/inst/doc/sentences.Rmd | 14 + cwbtools-0.3.3/cwbtools/inst/doc/sentences.html | 28 +- cwbtools-0.3.3/cwbtools/inst/doc/vignette.R | 27 +- cwbtools-0.3.3/cwbtools/inst/doc/vignette.Rmd | 27 +- cwbtools-0.3.3/cwbtools/inst/doc/vignette.html | 208 +++++++++---------- cwbtools-0.3.3/cwbtools/man/pkg_utils.Rd | 3 cwbtools-0.3.3/cwbtools/tests/testthat/test_encode.R | 1 cwbtools-0.3.3/cwbtools/vignettes/opennlp.Rmd | 10 cwbtools-0.3.3/cwbtools/vignettes/sentences.Rmd | 14 + cwbtools-0.3.3/cwbtools/vignettes/vignette.Rmd | 27 +- 25 files changed, 344 insertions(+), 250 deletions(-)
Title: Inferring Causal Effects using Bayesian Structural Time-Series
Models
Description: Implements a Bayesian approach to causal impact estimation in time
series, as described in Brodersen et al. (2015) <DOI:10.1214/14-AOAS788>.
See the package documentation on GitHub
<https://google.github.io/CausalImpact/> to get started.
Author: Kay H. Brodersen <kbrodersen@google.com>,
Alain Hauser <alhauser@google.com>
Maintainer: Alain Hauser <alhauser@google.com>
Diff between CausalImpact versions 1.2.5 dated 2021-01-04 and 1.2.6 dated 2021-02-23
DESCRIPTION | 8 MD5 | 8 README.md | 4 inst/doc/CausalImpact.html | 829 ++++++++++++---------------------- tests/testthat/test-impact-analysis.R | 4 5 files changed, 327 insertions(+), 526 deletions(-)
Title: Evaluating Multinomial Order Restrictions with Bridge Sampling
Description: Evaluate hypotheses concerning the distribution of multinomial
proportions using bridge sampling. The bridge sampling routine is able to
compute Bayes factors for hypotheses that entail inequality constraints,
equality constraints, free parameters, and mixtures of all three. These
hypotheses are tested against the encompassing hypothesis, that all parameters
vary freely or against the null hypothesis that all category proportions are equal.
For more information see Sarafoglou et al. (2020) <doi:10.31234/osf.io/bux7p>.
Author: Alexandra Sarafoglou [aut, cre]
(<https://orcid.org/0000-0003-0031-685X>),
Frederik Aust [aut] (<https://orcid.org/0000-0003-4900-788X>),
Julia M. Haaf [aut] (<https://orcid.org/0000-0001-5122-706X>),
Joris Goosen [aut],
Quentin F. Gronau [aut],
Maarten Marsman [aut] (<https://orcid.org/0000-0001-5309-7502>)
Maintainer: Alexandra Sarafoglou <alexandra.sarafoglou@gmail.com>
Diff between multibridge versions 1.0.0 dated 2021-01-25 and 1.1.0 dated 2021-02-23
DESCRIPTION | 8 +- MD5 | 22 +++---- NEWS.md | 4 + R/bmult_equalities_binom.R | 48 ++++++++++++----- R/bmult_equalities_mult.R | 20 ------- R/check_user_input.R | 52 ++++++++++++++++++ R/data_journals.R | 2 build/partial.rdb |binary inst/REFERENCES.bib | 62 ++++++++++++++++++++++ man/binom_bf_equality.Rd | 8 ++ man/journals.Rd | 2 tests/testthat/testthat-bayesfactors_equalities.R | 18 ++++++ 12 files changed, 196 insertions(+), 50 deletions(-)
Title: Interface for 'XGBoost' on 'Apache Spark'
Description: A 'sparklyr' <https://spark.rstudio.com/> extension that provides an R
interface for 'XGBoost' <https://github.com/dmlc/xgboost> on 'Apache Spark'. 'XGBoost' is an
optimized distributed gradient boosting library.
Author: Kevin Kuo [aut] (<https://orcid.org/0000-0001-7803-7901>),
Yitao Li [aut, cre] (<https://orcid.org/0000-0002-1261-905X>)
Maintainer: Yitao Li <yitao@rstudio.com>
Diff between sparkxgb versions 0.1.0 dated 2019-03-13 and 0.1.1 dated 2021-02-23
DESCRIPTION | 28 ++-- MD5 | 29 ++-- NAMESPACE | 2 R/dependencies.R | 17 ++ R/xgboost_classifier.R | 195 ++++++++++++++++--------------- R/xgboost_regressor.R | 13 -- README.md | 35 ++--- inst/java/sparkxgb-2.3-2.11.jar |binary inst/java/sparkxgb-2.4-2.11.jar |only inst/java/sparkxgb-2.4-2.12.jar |only inst/java/sparkxgb-3.0-2.12.jar |only man/xgboost_classifier.Rd | 89 ++++++++------ man/xgboost_regressor.Rd | 82 +++++++------ tests/testthat.R | 5 tests/testthat/derby.log |only tests/testthat/logs |only tests/testthat/test-xgboost-classifier.R | 32 ++++- 17 files changed, 303 insertions(+), 224 deletions(-)
Title: Rational Approximations of Fractional Stochastic Partial
Differential Equations
Description: Functions that compute rational approximations of fractional elliptic stochastic partial differential equations. The package also contains functions for common statistical usage of these approximations. The main reference for the methods is Bolin and Kirchner (2020) <doi:10.1080/10618600.2019.1665537>, which can be generated by the citation function in R.
Author: David Bolin [cre, aut]
Maintainer: David Bolin <davidbolin@gmail.com>
Diff between rSPDE versions 0.4.8 dated 2020-03-08 and 0.6.2 dated 2021-02-23
DESCRIPTION | 16 +++++---- MD5 | 15 ++++----- NEWS.md |only build/vignette.rds |binary inst/CITATION | 13 ++++--- inst/doc/rspde.R | 86 +++++++++++++++++++++++++++------------------------- inst/doc/rspde.Rmd | 16 ++++++--- inst/doc/rspde.html | 14 +++----- vignettes/rspde.Rmd | 16 ++++++--- 9 files changed, 95 insertions(+), 81 deletions(-)
Title: Easy Web Scraping
Description: The goal of 'ralger' is to facilitate web scraping in R.
Author: Mohamed El Fodil Ihaddaden [aut, cre],
Ezekiel Ogundepo [ctb],
Romain François [ctb]
Maintainer: Mohamed El Fodil Ihaddaden <ihaddaden.fodeil@gmail.com>
Diff between ralger versions 2.2.2 dated 2021-02-18 and 2.2.3 dated 2021-02-23
DESCRIPTION | 6 - MD5 | 22 +++--- NEWS.md | 5 + README.md | 97 +++++++++++++----------------- inst/doc/Functions_Overview.html | 105 ++++++++++++++++++++------------- tests/testthat/test-paragraphs_scrap.R | 14 +--- tests/testthat/test-preview_images.R | 1 tests/testthat/test-scrap.R | 1 tests/testthat/test-table_scrap.R | 2 tests/testthat/test-tidy_scrap.R | 3 tests/testthat/test-titles_scrap.R | 13 +--- tests/testthat/test-weblink_scrap.R | 1 12 files changed, 139 insertions(+), 131 deletions(-)
Title: Interface to 'OxCal' Radiocarbon Calibration
Description: A set of tools that enables using 'OxCal' from within R. 'OxCal' (<https://c14.arch.ox.ac.uk/oxcal.html>) is a standard archaeological tool intended to provide 14C calibration and analysis of archaeological and environmental chronological information. 'OxcAAR' allows simple calibration with 'Oxcal' and plotting of the results as well as the execution of sophisticated ('OxCal') code and the import of the results of bulk analysis and complex Bayesian sequential calibration.
Author: Hinz Martin [aut, cre],
Clemens Schmid [aut],
Daniel Knitter [aut],
Carolin Tietze [aut]
Maintainer: Hinz Martin <martin.hinz@iaw.unibe.ch>
Diff between oxcAAR versions 1.0.0 dated 2018-02-09 and 1.1.0 dated 2021-02-23
DESCRIPTION | 19 MD5 | 68 +-- NAMESPACE | 15 R/getter_functions.R | 72 +++ R/oxcAARCalibratedDate.R | 370 ++++++++++++++++-- R/oxcAARCalibratedDatesList.R | 141 +++++-- R/parsing_functions.R | 359 +++++++++++++---- R/tidy_output.R | 4 R/utility_functions.R | 54 ++ README.md | 31 + build/vignette.rds |binary inst/doc/basic-usage.R | 23 - inst/doc/basic-usage.Rmd | 1 inst/doc/basic-usage.html | 481 ++++++++++++++---------- man/Boundary.Rd |only man/Phase.Rd |only man/Sequence.Rd |only man/calcurve_plot.Rd | 8 man/get_bp.Rd | 13 man/get_cal_curve.Rd | 13 man/get_name.Rd | 13 man/get_posterior_probabilities.Rd |only man/get_posterior_sigma_ranges.Rd |only man/get_raw_probabilities.Rd | 12 man/get_sigma_ranges.Rd | 13 man/get_std.Rd | 13 man/oxcAARCalibratedDate.Rd | 19 man/oxcalSumSim.Rd | 9 man/quickSetupOxcal.Rd | 5 man/wrap_in_boundaries.Rd |only tests/testthat/Rplots.pdf |binary tests/testthat/test_calibrate.R | 7 tests/testthat/test_oxcaarcalibrateddateslist.R | 2 tests/testthat/test_parsing_functions.R | 15 tests/testthat/test_simulate.R | 6 tests/testthat/test_tidy_output.R | 8 tests/testthat/test_utility_functions.R | 19 vignettes/basic-usage.Rmd | 1 38 files changed, 1366 insertions(+), 448 deletions(-)
Title: Add Custom Legends to 'leaflet' Maps
Description: Provides extensions to the 'leaflet' package to
customize legends with images, text styling, orientation, sizing,
and symbology.
Author: Thomas Roh [aut, cre]
Maintainer: Thomas Roh <thomas@roh.engineering>
Diff between leaflegend versions 0.1.0 dated 2021-01-25 and 0.2.0 dated 2021-02-23
DESCRIPTION | 11 - MD5 | 16 +- NAMESPACE | 3 NEWS.md | 17 ++ R/legend.R | 375 ++++++++++++++++++++++++++++++++++++++++++++------ README.md | 12 + inst |only man/addLeafLegends.Rd | 20 ++ man/addLegendSize.Rd |only man/makeSymbol.Rd | 25 ++- 10 files changed, 418 insertions(+), 61 deletions(-)
Title: Space-Filling Random and Quasi-Random Sequences
Description: Generates random and quasi-random space-filling sequences. Supports the following sequences: 'Halton', 'Sobol', 'Owen'-scrambled 'Sobol', 'Owen'-scrambled 'Sobol' with errors distributed as blue noise, progressive jittered, progressive multi-jittered ('PMJ'), 'PMJ' with blue noise, 'PMJ02', and 'PMJ02' with blue noise. Includes a 'C++' 'API'. Methods derived from "Constructing Sobol sequences with better two-dimensional projections" (2012) <doi:10.1137/070709359> S. Joe and F. Y. Kuo, "Progressive Multi-Jittered Sample Sequences" (2018) <https://graphics.pixar.com/library/ProgressiveMultiJitteredSampling/paper.pdf> Christensen, P., Kensler, A. and Kilpatrick, C., and "A Low-Discrepancy Sampler that Distributes Monte Carlo Errors as a Blue Noise in Screen Space" (2019) E. Heitz, B. Laurent, O. Victor, C. David and I. Jean-Claude, <doi:10.1145/3306307.3328191>.
Author: Tyler Morgan-Wall [aut, cph, cre]
(<https://orcid.org/0000-0002-3131-3814>),
Andrew Helmer [ctb, cph],
Leonhard Grünschloß [ctb, cph],
Eric Heitz [ctb, cph]
Maintainer: Tyler Morgan-Wall <tylermw@gmail.com>
Diff between spacefillr versions 0.1.0 dated 2021-02-17 and 0.2.0 dated 2021-02-23
spacefillr-0.1.0/spacefillr/man/figures |only spacefillr-0.1.0/spacefillr/man/generate_sobol_owen_fast_set.Rd |only spacefillr-0.2.0/spacefillr/DESCRIPTION | 16 spacefillr-0.2.0/spacefillr/LICENSE | 2 spacefillr-0.2.0/spacefillr/MD5 | 41 spacefillr-0.2.0/spacefillr/NAMESPACE | 1 spacefillr-0.2.0/spacefillr/R/RcppExports.R | 8 spacefillr-0.2.0/spacefillr/R/generate_values.R | 35 spacefillr-0.2.0/spacefillr/inst/include/pj.h | 2 spacefillr-0.2.0/spacefillr/inst/include/pmj.h | 4 spacefillr-0.2.0/spacefillr/inst/include/pmj02.h | 4 spacefillr-0.2.0/spacefillr/inst/include/samplerBlueNoise.h |only spacefillr-0.2.0/spacefillr/inst/include/single_sample.h | 4 spacefillr-0.2.0/spacefillr/inst/include/sobol.h | 256 spacefillr-0.2.0/spacefillr/inst/include/sobolmatrices.h |18073 ---------- spacefillr-0.2.0/spacefillr/inst/include/util.h | 2 spacefillr-0.2.0/spacefillr/src/Makevars | 2 spacefillr-0.2.0/spacefillr/src/RcppExports.cpp | 24 spacefillr-0.2.0/spacefillr/src/generate_point_functions.cpp | 25 19 files changed, 149 insertions(+), 18350 deletions(-)
Title: Subgroup Discovery and Analytics
Description: A collection of efficient and effective tools and
algorithms for subgroup discovery and analytics. The package
integrates an R interface to the org.vikamine.kernel library
of the VIKAMINE system <http://www.vikamine.org> implementing
subgroup discovery, pattern mining and analytics in Java.
Author: Martin Atzmueller
Maintainer: Martin Atzmueller <martin@atzmueller.net>
Diff between rsubgroup versions 1.0 dated 2020-04-22 and 1.1 dated 2021-02-23
DESCRIPTION | 17 ++++++++++------- MD5 | 18 +++++++++--------- NEWS | 13 ++++++++++++- R/classes.R | 7 +++++-- R/subgroup.R | 15 ++++++++++++--- data/credit.data.rda |binary inst/java/subgroup.jar |binary java/readme-subgroup-jar.txt | 2 +- man/SDTaskConfig-class.Rd | 7 +++++++ tests/test.R | 12 +++++++++++- 10 files changed, 67 insertions(+), 24 deletions(-)
Title: Automatic Phenotyping of Electronic Health Record at Visit
Resolution
Description: Using Electronic Health Record (EHR) is difficult because most of the time the true characteristic of the patient is not available. Instead we can retrieve the International Classification of Disease code related to the disease of interest or we can count the occurrence of the Unified Medical Language System. None of them is the true phenotype which needs chart review to identify. However chart review is time consuming and costly. 'PheVis' is an algorithm which is phenotyping (i.e identify a characteristic) at the visit level in an unsupervised fashion. It can be used for chronic or acute diseases. An example of how to use 'PheVis' is available in the vignette. Basically there are two functions that are to be used: `train_phevis()` which trains the algorithm and `test_phevis()` which get the predicted probabilities. The detailed method is described in preprint by Ferté et al. (2020) <doi:10.1101/2020.06.15.20131458>.
Author: Thomas Ferte [aut, cre],
Boris P. Hejblum [aut]
Maintainer: Thomas Ferte <thomas.ferte@u-bordeaux.fr>
Diff between PheVis versions 1.0.1 dated 2021-02-16 and 1.0.2 dated 2021-02-23
DESCRIPTION | 6 +++--- MD5 | 6 +++--- NEWS.md | 5 +++++ tests/testthat/test-traintest_phevis.R | 9 +++++++-- 4 files changed, 18 insertions(+), 8 deletions(-)
Title: Mixed Data Sampling Regression
Description: Methods and tools for mixed frequency time series data analysis.
Allows estimation, model selection and forecasting for MIDAS regressions.
Author: Virmantas Kvedaras <virmantas.kvedaras@ec.europa.eu>, Vaidotas Zemlys-Balevicius
<zemlys@gmail.com>
Maintainer: Vaidotas Zemlys-Balevičius <zemlys@gmail.com>
Diff between midasr versions 0.7 dated 2019-03-05 and 0.8 dated 2021-02-23
DESCRIPTION | 12 +-- MD5 | 96 ++++++++++++------------- NEWS | 4 + R/midasr-package.R | 21 ++--- R/midasreg.R | 2 README.md | 10 +- man/UScpiqs.Rd | 8 +- man/USeffrw.Rd | 6 + man/USpayems.Rd | 6 + man/USqgdp.Rd | 6 + man/USrealgdp.Rd | 9 +- man/USunempr.Rd | 6 + man/amidas_table.Rd | 18 ++++ man/amweights.Rd | 1 man/average_forecast.Rd | 13 ++- man/coef.midas_nlpr.Rd | 3 man/coef.midas_sp.Rd | 3 man/extract.midas_r.Rd | 9 +- man/forecast.midas_r.Rd | 16 +++- man/hf_lags_table.Rd | 15 +++- man/imidas_r.Rd | 10 ++ man/lf_lags_table.Rd | 15 +++- man/midas_auto_sim.Rd | 12 ++- man/midas_lstr_plain.Rd | 13 ++- man/midas_lstr_sim.Rd | 14 +++ man/midas_mmm_plain.Rd | 13 ++- man/midas_mmm_sim.Rd | 14 +++ man/midas_pl_plain.Rd | 15 +++- man/midas_pl_sim.Rd | 13 ++- man/midas_qr.Rd | 12 ++- man/midas_r.Rd | 10 ++ man/midas_r_ic_table.Rd | 15 +++- man/midas_r_plain.Rd | 13 ++- man/midas_si_plain.Rd | 14 +++ man/midas_si_sim.Rd | 13 ++- man/midas_sp.Rd | 3 man/modsel.Rd | 9 +- man/oos_prec.Rd | 4 - man/plot_midas_coef.midas_nlpr.Rd | 10 ++ man/plot_midas_coef.midas_r.Rd | 10 ++ man/rvsp500.Rd | 8 +- man/select_and_forecast.Rd | 23 ++++-- man/simulate.midas_r.Rd | 16 +++- man/weights_table.Rd | 13 ++- tests/testthat/test_methods.R | 8 +- tests/testthat/test_midas_nlpr.R | 46 +++++++----- tests/testthat/test_midas_sp.R | 44 ++++++----- tests/testthat/test_midaslag.R | 10 +- tests/testthat/test_midasr.R | 142 +++++++++++++++++++------------------- 49 files changed, 533 insertions(+), 273 deletions(-)
Title: Bayesian Meta-Analysis and Network Meta-Analysis
Description: Contains functions performing Bayesian inference for meta-analytic and network meta-analytic models through Markov chain Monte Carlo algorithm. Currently, the package implements Yao, Kim, Chen, Ibrahim, Shah, and Jianxin Lin (2015) <doi:10.1080/01621459.2015.1006065> and network meta-regression models using heavy-tailed multivariate random effects with covariate-dependent variances. For maximal computational efficiency, the Markov chain Monte Carlo samplers for each model, written in C++, are fine-tuned. This software has been developed under the auspices of the National Institutes of Health and Merck & Co., Inc., Kenilworth, NJ, USA.
Author: Daeyoung Lim [aut, cre],
Ming-Hui Chen [ctb],
Sungduk Kim [ctb],
Joseph Ibrahim [ctb],
Arvind Shah [ctb],
Jianxin Lin [ctb]
Maintainer: Daeyoung Lim <daeyoung.lim@uconn.edu>
Diff between metapack versions 0.1.0 dated 2021-02-17 and 0.1.1 dated 2021-02-23
DESCRIPTION | 6 MD5 | 30 NEWS.md | 5 R/RcppExports.R | 190 ++--- R/bayes.parobs.R | 30 R/hpd.R | 2 build/vignette.rds |binary inst/doc/intro-to-metapack.R | 8 inst/doc/intro-to-metapack.html | 1276 +++++++++++++++++++++------------------- man/bayes.parobs.Rd | 22 man/hpd.Rd | 2 src/Makevars.win | 4 src/dic_nmr.cpp | 5 src/lpml_nmr.cpp | 5 src/random.cpp | 19 src/random.h | 6 16 files changed, 834 insertions(+), 776 deletions(-)
Title: Historical and Ahistorical Population Projection Matrix Analysis
Description: Creates matrix population models for use in population ecological
analyses. Specializes on the construction of historical matrices,
which are 2d matrices comprising 3 consecutive times of demographic
information. Estimates both raw and function-based forms of
historical and standard ahistorical matrices. It also estimates
function-based age-by-stage matrices. Methodology based on
Ehrlen (2000) <doi:10.1890/0012-9658(2000)081[1675:TDOPPD]2.0.CO;2>.
Author: Richard P. Shefferson [aut, cre]
(<https://orcid.org/0000-0002-5234-3131>),
Johan Ehrlen [aut] (<https://orcid.org/0000-0001-8539-8967>)
Maintainer: Richard P. Shefferson <cdorm@g.ecc.u-tokyo.ac.jp>
Diff between lefko3 versions 3.2.0 dated 2021-01-06 and 3.3.1 dated 2021-02-23
lefko3-3.2.0/lefko3/vignettes/Ch2.43-1.png |only lefko3-3.2.0/lefko3/vignettes/Ch5.27-1.png |only lefko3-3.2.0/lefko3/vignettes/Ch5.29-1.png |only lefko3-3.2.0/lefko3/vignettes/Ch5.34-1.png |only lefko3-3.2.0/lefko3/vignettes/Ch5.6-1.png |only lefko3-3.2.0/lefko3/vignettes/Ch6.29-1.png |only lefko3-3.3.1/lefko3/DESCRIPTION | 14 lefko3-3.3.1/lefko3/MD5 | 173 lefko3-3.3.1/lefko3/NAMESPACE | 4 lefko3-3.3.1/lefko3/NEWS | 46 lefko3-3.3.1/lefko3/R/RcppExports.R | 147 lefko3-3.3.1/lefko3/R/data.R | 53 lefko3-3.3.1/lefko3/R/datamanag.R | 220 lefko3-3.3.1/lefko3/R/errorchecks.R | 47 lefko3-3.3.1/lefko3/R/lefko3-package.R | 10 lefko3-3.3.1/lefko3/R/matrixcreation.R | 1149 +++- lefko3-3.3.1/lefko3/R/modelselection.R | 5609 ++++++++++++++++++++--- lefko3-3.3.1/lefko3/R/popchar.R | 1201 ++++ lefko3-3.3.1/lefko3/R/popdyn.R | 663 ++ lefko3-3.3.1/lefko3/build/vignette.rds |binary lefko3-3.3.1/lefko3/inst/CITATION | 13 lefko3-3.3.1/lefko3/inst/doc/Chapter1.Rmd | 114 lefko3-3.3.1/lefko3/inst/doc/Chapter1.html | 311 - lefko3-3.3.1/lefko3/inst/doc/Chapter2.Rmd | 251 - lefko3-3.3.1/lefko3/inst/doc/Chapter2.html | 1523 ++---- lefko3-3.3.1/lefko3/inst/doc/Chapter5.Rmd | 838 +-- lefko3-3.3.1/lefko3/inst/doc/Chapter5.html | 1371 ++--- lefko3-3.3.1/lefko3/inst/doc/Chapter6.Rmd | 477 - lefko3-3.3.1/lefko3/inst/doc/Chapter6.html | 1604 ++---- lefko3-3.3.1/lefko3/man/aflefko2.Rd | 112 lefko3-3.3.1/lefko3/man/cond_hmpm.Rd | 2 lefko3-3.3.1/lefko3/man/cypdata.Rd | 30 lefko3-3.3.1/lefko3/man/cypvert.Rd | 21 lefko3-3.3.1/lefko3/man/elasticity3.Rd | 18 lefko3-3.3.1/lefko3/man/elasticity3.lefkoMat.Rd | 66 lefko3-3.3.1/lefko3/man/elasticity3.list.Rd |only lefko3-3.3.1/lefko3/man/elasticity3.matrix.Rd | 16 lefko3-3.3.1/lefko3/man/flefko2.Rd | 114 lefko3-3.3.1/lefko3/man/flefko3.Rd | 123 lefko3-3.3.1/lefko3/man/historicalize3.Rd | 36 lefko3-3.3.1/lefko3/man/lambda3.Rd | 2 lefko3-3.3.1/lefko3/man/lambda3.lefkoMat.Rd | 3 lefko3-3.3.1/lefko3/man/lambda3.matrix.Rd | 2 lefko3-3.3.1/lefko3/man/lathyrus.Rd | 2 lefko3-3.3.1/lefko3/man/lefko3.Rd | 10 lefko3-3.3.1/lefko3/man/modelsearch.Rd | 28 lefko3-3.3.1/lefko3/man/overwrite.Rd | 7 lefko3-3.3.1/lefko3/man/parasearch.Rd |only lefko3-3.3.1/lefko3/man/repvalue3.Rd | 2 lefko3-3.3.1/lefko3/man/repvalue3.lefkoMat.Rd | 2 lefko3-3.3.1/lefko3/man/repvalue3.matrix.Rd | 2 lefko3-3.3.1/lefko3/man/rlefko2.Rd | 100 lefko3-3.3.1/lefko3/man/rlefko3.Rd | 111 lefko3-3.3.1/lefko3/man/sensitivity3.Rd | 18 lefko3-3.3.1/lefko3/man/sensitivity3.lefkoMat.Rd | 63 lefko3-3.3.1/lefko3/man/sensitivity3.list.Rd |only lefko3-3.3.1/lefko3/man/sensitivity3.matrix.Rd | 19 lefko3-3.3.1/lefko3/man/sf_create.Rd | 3 lefko3-3.3.1/lefko3/man/sf_distrib.Rd | 18 lefko3-3.3.1/lefko3/man/slambda3.Rd | 20 lefko3-3.3.1/lefko3/man/stablestage3.Rd | 2 lefko3-3.3.1/lefko3/man/stablestage3.lefkoMat.Rd | 6 lefko3-3.3.1/lefko3/man/stablestage3.matrix.Rd | 2 lefko3-3.3.1/lefko3/man/summary.lefkoCondMat.Rd | 45 lefko3-3.3.1/lefko3/man/supplemental.Rd |only lefko3-3.3.1/lefko3/man/verticalize3.Rd | 52 lefko3-3.3.1/lefko3/src/DataManagement.cpp | 642 +- lefko3-3.3.1/lefko3/src/ErrorChecks.cpp | 8 lefko3-3.3.1/lefko3/src/MatrixEstimators.cpp | 185 lefko3-3.3.1/lefko3/src/ModelSelection.cpp | 38 lefko3-3.3.1/lefko3/src/RcppExports.cpp | 53 lefko3-3.3.1/lefko3/src/popdynamics.cpp | 658 ++ lefko3-3.3.1/lefko3/vignettes/Ch2.21-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch2.21-2.png |only lefko3-3.3.1/lefko3/vignettes/Ch2.36-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch2.38-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch2.44-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch2.44-2.png |only lefko3-3.3.1/lefko3/vignettes/Ch2.45-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch2.46-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.24-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.24-2.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.28-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.30-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch5.31-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.35-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch5.36-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch5.37-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch5.5-1.png |binary lefko3-3.3.1/lefko3/vignettes/Ch6.18-1.png |only lefko3-3.3.1/lefko3/vignettes/Ch6.18-2.png |only lefko3-3.3.1/lefko3/vignettes/Chapter1.Rmd | 114 lefko3-3.3.1/lefko3/vignettes/Chapter2.Rmd | 251 - lefko3-3.3.1/lefko3/vignettes/Chapter2.Rmd.orig | 225 lefko3-3.3.1/lefko3/vignettes/Chapter5.Rmd | 838 +-- lefko3-3.3.1/lefko3/vignettes/Chapter5.Rmd.orig | 213 lefko3-3.3.1/lefko3/vignettes/Chapter6.Rmd | 477 - lefko3-3.3.1/lefko3/vignettes/Chapter6.Rmd.orig | 169 lefko3-3.3.1/lefko3/vignettes/Lefko3Tutorial.bib | 4 99 files changed, 13719 insertions(+), 7051 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>),
Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>),
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 1.0.0 dated 2021-01-08 and 1.0.1 dated 2021-02-23
DESCRIPTION | 6 MD5 | 236 ++--- NAMESPACE | 58 - NEWS.md | 266 +++--- R/BayesMallows.R | 64 - R/Lik_DB_MIX.R | 137 +-- R/RcppExports.R | 386 ++++----- R/assess_convergence.R | 396 ++++----- R/assign_cluster.R | 164 +-- R/compute_consensus.R | 414 ++++----- R/compute_mallows.R | 848 ++++++++++---------- R/compute_mallows_mixtures.R | 90 +- R/compute_posterior_intervals.R | 256 +++--- R/data.R | 62 - R/estimate_partition_function.R | 214 ++--- R/expected_dist.R | 100 +- R/generate_constraints.R | 162 +-- R/generate_initial_ranking.R | 116 +- R/generate_transitive_closure.R | 214 ++--- R/label_switching.R | 42 R/misc.R | 144 +-- R/misc_expected_dist.R | 222 ++--- R/misc_likelihood.R | 142 +-- R/obs_freq.R | 24 R/plot.BayesMallows.R | 282 +++--- R/plot_elbow.R | 134 +-- R/plot_top_k.R | 168 +-- R/predict_top_k.R | 126 +- R/print.BayesMallows.R | 52 - R/print.BayesMallowsMixtures.R | 58 - R/rank_conversion.R | 178 ++-- R/rank_distance.R | 80 - R/rank_freq_distr.R | 56 - R/sample_mallows.R | 284 +++--- R/tidy_mcmc.R | 506 +++++------ build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 30 inst/REFERENCES.bib | 564 ++++++------- inst/doc/BayesMallows.pdf.asis | 4 inst/examples/Lik_DB_MIX_example.R | 95 +- inst/examples/compute_consensus_example.R | 128 +-- inst/examples/compute_mallows_example.R | 240 ++--- inst/examples/compute_mallows_mixtures_example.R | 122 +- inst/examples/compute_posterior_intervals_example.R | 56 - inst/examples/estimate_partition_function_example.R | 130 +-- inst/examples/expected_dist_example.R | 12 inst/examples/generate_constraints_example.R | 42 inst/examples/generate_initial_ranking_example.R | 78 - inst/examples/generate_transitive_closure_example.R | 106 +- inst/examples/label_switching_example.R | 150 +-- inst/examples/obs_freq_example.R | 230 ++--- inst/examples/plot.BayesMallows_example.R | 98 +- inst/examples/plot_top_k_example.R | 42 inst/examples/rank_distance_example.R | 30 inst/examples/rank_freq_distr_example.R | 12 inst/examples/sample_mallows_example.R | 98 +- man/BayesMallows.Rd | 66 - man/assess_convergence.Rd | 76 - man/assign_cluster.Rd | 90 +- man/asymptotic_partition_function.Rd | 82 - man/beach_preferences.Rd | 38 man/compute_consensus.Rd | 214 ++--- man/compute_importance_sampling_estimate.Rd | 56 - man/compute_mallows.Rd | 726 ++++++++--------- man/compute_mallows_mixtures.Rd | 180 ++-- man/compute_posterior_intervals.Rd | 154 +-- man/dot-generate_transitive_closure.Rd | 32 man/estimate_partition_function.Rd | 270 +++--- man/expected_dist.Rd | 58 - man/generate_constraints.Rd | 112 +- man/generate_initial_ranking.Rd | 144 +-- man/generate_transitive_closure.Rd | 204 ++-- man/get_partition_function.Rd | 76 - man/get_rank_distance.Rd | 68 - man/label_switching.Rd | 198 ++-- man/lik_db_mix.Rd | 189 ++-- man/log_expected_dist.Rd | 50 - man/obs_freq.Rd | 260 +++--- man/plot.BayesMallows.Rd | 162 +-- man/plot_elbow.Rd | 188 ++-- man/plot_top_k.Rd | 116 +- man/potato_true_ranking.Rd | 38 man/potato_visual.Rd | 42 man/potato_weighing.Rd | 42 man/predict_top_k.Rd | 64 - man/print.BayesMallows.Rd | 34 man/print.BayesMallowsMixtures.Rd | 34 man/rank_conversion.Rd | 120 +- man/rank_distance.Rd | 106 +- man/rank_freq_distr.Rd | 60 - man/rmallows.Rd | 94 +- man/run_mcmc.Rd | 218 ++--- man/sample_mallows.Rd | 238 ++--- man/sushi_rankings.Rd | 40 man/validate_permutation.Rd | 36 tests/testthat.R | 10 tests/testthat/test-Lik_DB_MIX.R | 122 +- tests/testthat/test-rank_freq_distr.R | 122 +- tests/testthat/test_assess_convergence.R | 28 tests/testthat/test_compute_consensus.R | 362 ++++---- tests/testthat/test_compute_mallows.R | 352 ++++---- tests/testthat/test_distance_function.R | 224 ++--- tests/testthat/test_estimate_partition_function.R | 88 +- tests/testthat/test_expected_dist.R | 30 tests/testthat/test_generate_ranking.R | 50 - tests/testthat/test_mcmc_function.R | 80 - tests/testthat/test_misc_cpp.R | 102 +- tests/testthat/test_misc_functions.R | 46 - tests/testthat/test_partition_function.R | 242 ++--- tests/testthat/test_plot.R | 20 tests/testthat/test_plot_elbow.R | 24 tests/testthat/test_plot_top_k.R | 164 +-- tests/testthat/test_print.R | 40 tests/testthat/test_random_number_seed.R | 100 +- tests/testthat/test_rank_conversion.R | 52 - tests/testthat/test_sample_mallows.R | 68 - tests/testthat/test_transitive_closure.R | 100 +- vignettes/BayesMallows.pdf.asis | 4 119 files changed, 8195 insertions(+), 8164 deletions(-)
Title: 'jQuery UI' Interactions and Effects for Shiny
Description: An extension to shiny that brings interactions and animation effects from
'jQuery UI' library.
Author: Yang Tang [aut, cre]
Maintainer: Yang Tang <tang_yang@outlook.com>
Diff between shinyjqui versions 0.3.3 dated 2020-02-03 and 0.4.0 dated 2021-02-23
shinyjqui-0.3.3/shinyjqui/R/includeJqueryUI.R |only shinyjqui-0.3.3/shinyjqui/man/includeJqueryUI.Rd |only shinyjqui-0.4.0/shinyjqui/DESCRIPTION | 11 shinyjqui-0.4.0/shinyjqui/MD5 | 110 +- shinyjqui-0.4.0/shinyjqui/NAMESPACE | 10 shinyjqui-0.4.0/shinyjqui/NEWS.md | 23 shinyjqui-0.4.0/shinyjqui/R/bookmarking.R |only shinyjqui-0.4.0/shinyjqui/R/effects.R | 122 -- shinyjqui-0.4.0/shinyjqui/R/icon.R | 2 shinyjqui-0.4.0/shinyjqui/R/interaction_S3.R |only shinyjqui-0.4.0/shinyjqui/R/interactions.R | 278 +----- shinyjqui-0.4.0/shinyjqui/R/orderInput.R | 246 +++++ shinyjqui-0.4.0/shinyjqui/R/position.R |only shinyjqui-0.4.0/shinyjqui/R/shinyjqui-package.R |only shinyjqui-0.4.0/shinyjqui/R/sortableTableOutput.R | 2 shinyjqui-0.4.0/shinyjqui/R/utils.R | 143 +++ shinyjqui-0.4.0/shinyjqui/README.md | 66 + shinyjqui-0.4.0/shinyjqui/build/vignette.rds |binary shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.R | 145 +-- shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.Rmd | 257 +++--- shinyjqui-0.4.0/shinyjqui/inst/doc/introduction.html | 424 +++++----- shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.R | 27 shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.Rmd | 46 - shinyjqui-0.4.0/shinyjqui/inst/doc/orderInput.html | 131 ++- shinyjqui-0.4.0/shinyjqui/inst/doc/save-and-restore.R | 39 shinyjqui-0.4.0/shinyjqui/inst/doc/save-and-restore.Rmd | 51 + shinyjqui-0.4.0/shinyjqui/inst/doc/save-and-restore.html | 209 +++- shinyjqui-0.4.0/shinyjqui/inst/shinydemos/effect_specific_options.R |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/flexdashboard.Rmd |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/flexdashboard.html |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/htmlwidget.R |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/htmlwidget.Rmd |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/htmlwidget.js |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/orderInput.R | 61 - shinyjqui-0.4.0/shinyjqui/inst/shinydemos/orderInputLegacy.R |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/orderInput_bookmarking.R | 8 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/position.R |only shinyjqui-0.4.0/shinyjqui/inst/shinydemos/resizable_combine_with_other_interactions.R | 6 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/sortable_bookmarking.R | 2 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/sortable_save_load.R | 2 shinyjqui-0.4.0/shinyjqui/inst/shinydemos/work_with_insertUI.R |only shinyjqui-0.4.0/shinyjqui/inst/www/jquery.ui.touch-punch.min.js |only shinyjqui-0.4.0/shinyjqui/inst/www/orderInputBinding.js |only shinyjqui-0.4.0/shinyjqui/inst/www/shinyjqui.js | 140 ++- shinyjqui-0.4.0/shinyjqui/inst/www/shinyjqui.min.js | 2 shinyjqui-0.4.0/shinyjqui/man/Animation_effects.Rd | 138 +-- shinyjqui-0.4.0/shinyjqui/man/Class_effects.Rd | 166 ++- shinyjqui-0.4.0/shinyjqui/man/Interactions.Rd | 386 ++++----- shinyjqui-0.4.0/shinyjqui/man/draggableModalDialog.Rd | 6 shinyjqui-0.4.0/shinyjqui/man/get_jqui_effects.Rd | 26 shinyjqui-0.4.0/shinyjqui/man/jqui_bookmarking.Rd | 4 shinyjqui-0.4.0/shinyjqui/man/jqui_icon.Rd | 58 - shinyjqui-0.4.0/shinyjqui/man/jqui_position.Rd |only shinyjqui-0.4.0/shinyjqui/man/orderInput.Rd | 85 +- shinyjqui-0.4.0/shinyjqui/man/reexports.Rd | 30 shinyjqui-0.4.0/shinyjqui/man/selectableTableOutput.Rd | 2 shinyjqui-0.4.0/shinyjqui/man/shinyjqui-package.Rd |only shinyjqui-0.4.0/shinyjqui/man/sortableCheckboxGroupInput.Rd | 4 shinyjqui-0.4.0/shinyjqui/man/sortableRadioButtons.Rd | 43 - shinyjqui-0.4.0/shinyjqui/man/sortableTableOutput.Rd | 2 shinyjqui-0.4.0/shinyjqui/man/sortableTabsetPanel.Rd | 15 shinyjqui-0.4.0/shinyjqui/man/updateOrderInput.Rd |only shinyjqui-0.4.0/shinyjqui/vignettes/fig/orderInput6.gif |only shinyjqui-0.4.0/shinyjqui/vignettes/fig/orderInput7.gif |only shinyjqui-0.4.0/shinyjqui/vignettes/introduction.Rmd | 257 +++--- shinyjqui-0.4.0/shinyjqui/vignettes/orderInput.Rmd | 46 - shinyjqui-0.4.0/shinyjqui/vignettes/save-and-restore.Rmd | 51 + 67 files changed, 2292 insertions(+), 1590 deletions(-)
Title: Interface (Wrapper) to MPI (Message-Passing Interface)
Description: An interface (wrapper) to MPI. It also
provides interactive R manager and worker environment.
Author: Hao Yu [aut]
Maintainer: Hao Yu <hyu@stats.uwo.ca>
Diff between Rmpi versions 0.6-9 dated 2018-11-13 and 0.6-9.1 dated 2021-02-23
DESCRIPTION | 10 ++--- MD5 | 70 ++++++++++++++++++++--------------------- R/Rmpi.R | 38 +++++++++++----------- man/mpi.abort.Rd | 2 - man/mpi.barrier.Rd | 2 - man/mpi.bcast.Rd | 2 - man/mpi.cart.coords.Rd | 2 - man/mpi.cart.create.Rd | 2 - man/mpi.cart.get.Rd | 2 - man/mpi.cart.rank.Rd | 2 - man/mpi.cart.shift.Rd | 2 - man/mpi.cartdim.get.Rd | 2 - man/mpi.comm.Rd | 2 - man/mpi.comm.disconnect.Rd | 2 - man/mpi.comm.free.Rd | 2 - man/mpi.comm.inter.Rd | 2 - man/mpi.comm.set.errhandler.Rd | 2 - man/mpi.comm.spawn.Rd | 2 - man/mpi.const.Rd | 2 - man/mpi.dims.create.Rd | 2 - man/mpi.finalize.Rd | 2 - man/mpi.gather.Rd | 2 - man/mpi.gather.Robj.Rd | 2 - man/mpi.get.count.Rd | 2 - man/mpi.get.processor.name.Rd | 2 - man/mpi.get.sourcetag.Rd | 2 - man/mpi.intercomm.merge.Rd | 2 - man/mpi.probe.Rd | 2 - man/mpi.realloc.Rd | 4 +- man/mpi.reduce.Rd | 2 - man/mpi.scatter.Rd | 2 - man/mpi.send.Rd | 2 - man/mpi.send.Robj.Rd | 2 - man/mpi.sendrecv.Rd | 2 - man/mpi.universe.size.Rd | 2 - man/mpi.wait.Rd | 2 - 36 files changed, 93 insertions(+), 93 deletions(-)
Title: Interface to Bank of Japan Statistics
Description: Provides an interface to data provided by the Bank of Japan
<https://www.boj.or.jp>.
Author: Stefan Angrick [aut, cre, cph]
Maintainer: Stefan Angrick <contact@stefanangrick.net>
Diff between BOJ versions 0.2.2 dated 2020-05-25 and 0.2.3 dated 2021-02-23
DESCRIPTION | 10 +- LICENSE | 2 MD5 | 14 +-- build/vignette.rds |binary inst/doc/BOJ.R | 24 +++-- inst/doc/BOJ.Rmd | 28 +++--- inst/doc/BOJ.html | 221 +++++++++++++++++++++++++++++++---------------------- vignettes/BOJ.Rmd | 28 +++--- 8 files changed, 187 insertions(+), 140 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-08 0.1.3
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-20 0.1.1
Title: Utilities Powering the Globe and Mail's Data Journalism Template
Description: Core functions necessary for using The Globe and Mail's R data journalism template, 'startr', along with utilities for day-to-day data journalism tasks, such as reading and writing files, producing graphics and cleaning up datasets.
Author: Tom Cardoso [aut, cre] (creator and maintainer),
Michael Pereira [ctb],
The Globe and Mail Inc. [cph]
Maintainer: Tom Cardoso <tcardoso@globeandmail.com>
Diff between upstartr versions 0.1.0 dated 2021-02-15 and 0.1.1 dated 2021-02-23
DESCRIPTION | 6 +++--- MD5 | 10 +++++----- NEWS.md | 7 +++++++ R/init.R | 2 +- R/write.R | 12 +++++------- man/write_plot.Rd | 5 ++++- 6 files changed, 25 insertions(+), 17 deletions(-)